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Sample records for allen brain atlas

  1. Neuroinformatics of the Allen Mouse Brain Connectivity Atlas.

    PubMed

    Kuan, Leonard; Li, Yang; Lau, Chris; Feng, David; Bernard, Amy; Sunkin, Susan M; Zeng, Hongkui; Dang, Chinh; Hawrylycz, Michael; Ng, Lydia

    2015-02-01

    The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. Anatomical trajectories throughout the brain were mapped into a common 3D space using a standardized platform to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. This connectivity atlas has several desirable features, including brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource, and an open-access public online database (http://connectivity.brain-map.org/). Meaningful informatics data quantification and comparison is key to effective use and interpretation of connectome data. This relies on successful definition of a high fidelity atlas template and framework, mapping precision of raw data sets into the 3D reference framework, accurate signal detection and quantitative connection strength algorithms, and effective presentation in an integrated online application. Here we describe key informatics pipeline steps in the creation of the Allen Mouse Brain Connectivity Atlas and include basic application use cases. PMID:25536338

  2. Allen Brain Atlas-Driven Visualizations: a web-based gene expression energy visualization tool.

    PubMed

    Zaldivar, Andrew; Krichmar, Jeffrey L

    2014-01-01

    The Allen Brain Atlas-Driven Visualizations (ABADV) is a publicly accessible web-based tool created to retrieve and visualize expression energy data from the Allen Brain Atlas (ABA) across multiple genes and brain structures. Though the ABA offers their own search engine and software for researchers to view their growing collection of online public data sets, including extensive gene expression and neuroanatomical data from human and mouse brain, many of their tools limit the amount of genes and brain structures researchers can view at once. To complement their work, ABADV generates multiple pie charts, bar charts and heat maps of expression energy values for any given set of genes and brain structures. Such a suite of free and easy-to-understand visualizations allows for easy comparison of gene expression across multiple brain areas. In addition, each visualization links back to the ABA so researchers may view a summary of the experimental detail. ABADV is currently supported on modern web browsers and is compatible with expression energy data from the Allen Mouse Brain Atlas in situ hybridization data. By creating this web application, researchers can immediately obtain and survey numerous amounts of expression energy data from the ABA, which they can then use to supplement their work or perform meta-analysis. In the future, we hope to enable ABADV across multiple data resources. PMID:24904397

  3. Computational neuroanatomy: mapping cell-type densities in the mouse brain, simulations from the Allen Brain Atlas

    NASA Astrophysics Data System (ADS)

    Grange, Pascal

    2015-09-01

    The Allen Brain Atlas of the adult mouse (ABA) consists of digitized expression profiles of thousands of genes in the mouse brain, co-registered to a common three-dimensional template (the Allen Reference Atlas).This brain-wide, genome-wide data set has triggered a renaissance in neuroanatomy. Its voxelized version (with cubic voxels of side 200 microns) is available for desktop computation in MATLAB. On the other hand, brain cells exhibit a great phenotypic diversity (in terms of size, shape and electrophysiological activity), which has inspired the names of some well-studied cell types, such as granule cells and medium spiny neurons. However, no exhaustive taxonomy of brain cell is available. A genetic classification of brain cells is being undertaken, and some cell types have been chraracterized by their transcriptome profiles. However, given a cell type characterized by its transcriptome, it is not clear where else in the brain similar cells can be found. The ABA can been used to solve this region-specificity problem in a data-driven way: rewriting the brain-wide expression profiles of all genes in the atlas as a sum of cell-type-specific transcriptome profiles is equivalent to solving a quadratic optimization problem at each voxel in the brain. However, the estimated brain-wide densities of 64 cell types published recently were based on one series of co-registered coronal in situ hybridization (ISH) images per gene, whereas the online ABA contains several image series per gene, including sagittal ones. In the presented work, we simulate the variability of cell-type densities in a Monte Carlo way by repeatedly drawing a random image series for each gene and solving the optimization problem. This yields error bars on the region-specificity of cell types.

  4. Exercises in Anatomy, Connectivity, and Morphology using Neuromorpho.org and the Allen Brain Atlas

    PubMed Central

    Chu, Philip; Peck, Joshua; Brumberg, Joshua C.

    2015-01-01

    Laboratory instruction of neuroscience is often limited by the lack of physical resources and supplies (e.g., brains specimens, dissection kits, physiological equipment). Online databases can serve as supplements to material labs by providing professionally collected images of brain specimens and their underlying cellular populations with resolution and quality that is extremely difficult to access for strictly pedagogical purposes. We describe a method using two online databases, the Neuromorpho.org and the Allen Brain Atlas (ABA), that freely provide access to data from working brain scientists that can be modified for laboratory instruction/exercises. Neuromorpho.org is the first neuronal morphology database that provides qualitative and quantitative data from reconstructed cells analyzed in published scientific reports. The Neuromorpho.org database contains cross species and multiple neuronal phenotype datasets which allows for comparative examinations. The ABA provides modules that allow students to study the anatomy of the rodent brain, as well as observe the different cellular phenotypes that exist using histochemical labeling. Using these tools in conjunction, advanced students can ask questions about qualitative and quantitative neuronal morphology, then examine the distribution of the same cell types across the entire brain to gain a full appreciation of the magnitude of the brain’s complexity. PMID:25838808

  5. Precise Anatomic Localization of Accumulated Lipids in Mfp2 Deficient Murine Brains Through Automated Registration of SIMS Images to the Allen Brain Atlas

    NASA Astrophysics Data System (ADS)

    Škrášková, Karolina; Khmelinskii, Artem; Abdelmoula, Walid M.; De Munter, Stephanie; Baes, Myriam; McDonnell, Liam; Dijkstra, Jouke; Heeren, Ron M. A.

    2015-06-01

    Mass spectrometry imaging (MSI) is a powerful tool for the molecular characterization of specific tissue regions. Histochemical staining provides anatomic information complementary to MSI data. The combination of both modalities has been proven to be beneficial. However, direct comparison of histology based and mass spectrometry-based molecular images can become problematic because of potential tissue damages or changes caused by different sample preparation. Curated atlases such as the Allen Brain Atlas (ABA) offer a collection of highly detailed and standardized anatomic information. Direct comparison of MSI brain data to the ABA allows for conclusions to be drawn on precise anatomic localization of the molecular signal. Here we applied secondary ion mass spectrometry imaging at high spatial resolution to study brains of knock-out mouse models with impaired peroxisomal β-oxidation. Murine models were lacking D-multifunctional protein (MFP2), which is involved in degradation of very long chain fatty acids. SIMS imaging revealed deposits of fatty acids within distinct brain regions. Manual comparison of the MSI data with the histologic stains did not allow for an unequivocal anatomic identification of the fatty acids rich regions. We further employed an automated pipeline for co-registration of the SIMS data to the ABA. The registration enabled precise anatomic annotation of the brain structures with the revealed lipid deposits. The precise anatomic localization allowed for a deeper insight into the pathology of Mfp2 deficient mouse models.

  6. Gene co-expression analysis identifies brain regions and cell types involved in migraine pathophysiology: a GWAS-based study using the Allen Human Brain Atlas.

    PubMed

    Eising, Else; Huisman, Sjoerd M H; Mahfouz, Ahmed; Vijfhuizen, Lisanne S; Anttila, Verneri; Winsvold, Bendik S; Kurth, Tobias; Ikram, M Arfan; Freilinger, Tobias; Kaprio, Jaakko; Boomsma, Dorret I; van Duijn, Cornelia M; Järvelin, Marjo-Riitta R; Zwart, John-Anker; Quaye, Lydia; Strachan, David P; Kubisch, Christian; Dichgans, Martin; Davey Smith, George; Stefansson, Kari; Palotie, Aarno; Chasman, Daniel I; Ferrari, Michel D; Terwindt, Gisela M; de Vries, Boukje; Nyholt, Dale R; Lelieveldt, Boudewijn P F; van den Maagdenberg, Arn M J M; Reinders, Marcel J T

    2016-04-01

    Migraine is a common disabling neurovascular brain disorder typically characterised by attacks of severe headache and associated with autonomic and neurological symptoms. Migraine is caused by an interplay of genetic and environmental factors. Genome-wide association studies (GWAS) have identified over a dozen genetic loci associated with migraine. Here, we integrated migraine GWAS data with high-resolution spatial gene expression data of normal adult brains from the Allen Human Brain Atlas to identify specific brain regions and molecular pathways that are possibly involved in migraine pathophysiology. To this end, we used two complementary methods. In GWAS data from 23,285 migraine cases and 95,425 controls, we first studied modules of co-expressed genes that were calculated based on human brain expression data for enrichment of genes that showed association with migraine. Enrichment of a migraine GWAS signal was found for five modules that suggest involvement in migraine pathophysiology of: (i) neurotransmission, protein catabolism and mitochondria in the cortex; (ii) transcription regulation in the cortex and cerebellum; and (iii) oligodendrocytes and mitochondria in subcortical areas. Second, we used the high-confidence genes from the migraine GWAS as a basis to construct local migraine-related co-expression gene networks. Signatures of all brain regions and pathways that were prominent in the first method also surfaced in the second method, thus providing support that these brain regions and pathways are indeed involved in migraine pathophysiology. PMID:26899160

  7. MENGA: A New Comprehensive Tool for the Integration of Neuroimaging Data and the Allen Human Brain Transcriptome Atlas

    PubMed Central

    Rizzo, Gaia; Veronese, Mattia; Expert, Paul; Turkheimer, Federico E.; Bertoldo, Alessandra

    2016-01-01

    Introduction Brain-wide mRNA mappings offer a great potential for neuroscience research as they can provide information about system proteomics. In a previous work we have correlated mRNA maps with the binding patterns of radioligands targeting specific molecular systems and imaged with positron emission tomography (PET) in unrelated control groups. This approach is potentially applicable to any imaging modality as long as an efficient procedure of imaging-genomic matching is provided. In the original work we considered mRNA brain maps of the whole human genome derived from the Allen human brain database (ABA) and we performed the analysis with a specific region-based segmentation with a resolution that was limited by the PET data parcellation. There we identified the need for a platform for imaging-genomic integration that should be usable with any imaging modalities and fully exploit the high resolution mapping of ABA dataset. Aim In this work we present MENGA (Multimodal Environment for Neuroimaging and Genomic Analysis), a software platform that allows the investigation of the correlation patterns between neuroimaging data of any sort (both functional and structural) with mRNA gene expression profiles derived from the ABA database at high resolution. Results We applied MENGA to six different imaging datasets from three modalities (PET, single photon emission tomography and magnetic resonance imaging) targeting the dopamine and serotonin receptor systems and the myelin molecular structure. We further investigated imaging-genomic correlations in the case of mismatch between selected proteins and imaging targets. PMID:26882227

  8. Brain templates and atlases.

    PubMed

    Evans, Alan C; Janke, Andrew L; Collins, D Louis; Baillet, Sylvain

    2012-08-15

    The core concept within the field of brain mapping is the use of a standardized, or "stereotaxic", 3D coordinate frame for data analysis and reporting of findings from neuroimaging experiments. This simple construct allows brain researchers to combine data from many subjects such that group-averaged signals, be they structural or functional, can be detected above the background noise that would swamp subtle signals from any single subject. Where the signal is robust enough to be detected in individuals, it allows for the exploration of inter-individual variance in the location of that signal. From a larger perspective, it provides a powerful medium for comparison and/or combination of brain mapping findings from different imaging modalities and laboratories around the world. Finally, it provides a framework for the creation of large-scale neuroimaging databases or "atlases" that capture the population mean and variance in anatomical or physiological metrics as a function of age or disease. However, while the above benefits are not in question at first order, there are a number of conceptual and practical challenges that introduce second-order incompatibilities among experimental data. Stereotaxic mapping requires two basic components: (i) the specification of the 3D stereotaxic coordinate space, and (ii) a mapping function that transforms a 3D brain image from "native" space, i.e. the coordinate frame of the scanner at data acquisition, to that stereotaxic space. The first component is usually expressed by the choice of a representative 3D MR image that serves as target "template" or atlas. The native image is re-sampled from native to stereotaxic space under the mapping function that may have few or many degrees of freedom, depending upon the experimental design. The optimal choice of atlas template and mapping function depend upon considerations of age, gender, hemispheric asymmetry, anatomical correspondence, spatial normalization methodology and disease

  9. High-resolution gene expression atlases for adult and developing mouse brain and spinal cord.

    PubMed

    Henry, Alex M; Hohmann, John G

    2012-10-01

    Knowledge of the structure, genetics, circuits, and physiological properties of the mammalian brain in both normal and pathological states is ever increasing as research labs worldwide probe the various aspects of brain function. Until recently, however, comprehensive cataloging of gene expression across the central nervous system has been lacking. The Allen Institute for Brain Science, as part of its mission to propel neuroscience research, has completed several large gene-mapping projects in mouse, nonhuman primate, and human brain, producing informative online public resources and tools. Here we present the Allen Mouse Brain Atlas, covering ~20,000 genes throughout the adult mouse brain; the Allen Developing Mouse Brain Atlas, detailing expression of approximately 2,000 important developmental genes across seven embryonic and postnatal stages of brain growth; and the Allen Spinal Cord Atlas, revealing expression for ~20,000 genes in the adult and neonatal mouse spinal cords. Integrated data-mining tools, including reference atlases, informatics analyses, and 3-D viewers, are described. For these massive-scale projects, high-throughput industrial techniques were developed to standardize and reliably repeat experimental goals. To verify consistency and accuracy, a detailed analysis of the 1,000 most viewed genes for the adult mouse brain (according to website page views) was performed by comparing our data with peer-reviewed literature and other databases. We show that our data are highly consistent with independent sources and provide a comprehensive compendium of information and tools used by thousands of researchers each month. All data and tools are freely available via the Allen Brain Atlas portal (www.brain-map.org). PMID:22832508

  10. An anatomic gene expression atlas of the adult mouse brain.

    PubMed

    Ng, Lydia; Bernard, Amy; Lau, Chris; Overly, Caroline C; Dong, Hong-Wei; Kuan, Chihchau; Pathak, Sayan; Sunkin, Susan M; Dang, Chinh; Bohland, Jason W; Bokil, Hemant; Mitra, Partha P; Puelles, Luis; Hohmann, John; Anderson, David J; Lein, Ed S; Jones, Allan R; Hawrylycz, Michael

    2009-03-01

    Studying gene expression provides a powerful means of understanding structure-function relationships in the nervous system. The availability of genome-scale in situ hybridization datasets enables new possibilities for understanding brain organization based on gene expression patterns. The Anatomic Gene Expression Atlas (AGEA) is a new relational atlas revealing the genetic architecture of the adult C57Bl/6J mouse brain based on spatial correlations across expression data for thousands of genes in the Allen Brain Atlas (ABA). The AGEA includes three discovery tools for examining neuroanatomical relationships and boundaries: (1) three-dimensional expression-based correlation maps, (2) a hierarchical transcriptome-based parcellation of the brain and (3) a facility to retrieve from the ABA specific genes showing enriched expression in local correlated domains. The utility of this atlas is illustrated by analysis of genetic organization in the thalamus, striatum and cerebral cortex. The AGEA is a publicly accessible online computational tool integrated with the ABA (http://mouse.brain-map.org/agea). PMID:19219037

  11. Multiple brain atlas database and atlas-based neuroimaging system.

    PubMed

    Nowinski, W L; Fang, A; Nguyen, B T; Raphel, J K; Jagannathan, L; Raghavan, R; Bryan, R N; Miller, G A

    1997-01-01

    For the purpose of developing multiple, complementary, fully labeled electronic brain atlases and an atlas-based neuroimaging system for analysis, quantification, and real-time manipulation of cerebral structures in two and three dimensions, we have digitized, enhanced, segmented, and labeled the following print brain atlases: Co-Planar Stereotaxic Atlas of the Human Brain by Talairach and Tournoux, Atlas for Stereotaxy of the Human Brain by Schaltenbrand and Wahren, Referentially Oriented Cerebral MRI Anatomy by Talairach and Tournoux, and Atlas of the Cerebral Sulci by Ono, Kubik, and Abernathey. Three-dimensional extensions of these atlases have been developed as well. All two- and three-dimensional atlases are mutually preregistered and may be interactively registered with an actual patient's data. An atlas-based neuroimaging system has been developed that provides support for reformatting, registration, visualization, navigation, image processing, and quantification of clinical data. The anatomical index contains about 1,000 structures and over 400 sulcal patterns. Several new applications of the brain atlas database also have been developed, supported by various technologies such as virtual reality, the Internet, and electronic publishing. Fusion of information from multiple atlases assists the user in comprehensively understanding brain structures and identifying and quantifying anatomical regions in clinical data. The multiple brain atlas database and atlas-based neuroimaging system have substantial potential impact in stereotactic neurosurgery and radiotherapy by assisting in visualization and real-time manipulation in three dimensions of anatomical structures, in quantitative neuroradiology by allowing interactive analysis of clinical data, in three-dimensional neuroeducation, and in brain function studies. PMID:9148878

  12. Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases

    PubMed Central

    Zaslavsky, Ilya; Baldock, Richard A.; Boline, Jyl

    2014-01-01

    Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today's data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems (SRSs) and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project. PMID

  13. A high resolution spatiotemporal atlas of gene expression of the developing mouse brain

    PubMed Central

    Thompson, Carol L.; Ng, Lydia; Menon, Vilas; Martinez, Salvador; Lee, Chang-Kyu; Glattfelder, Katie; Sunkin, Susan M.; Henry, Alex; Lau, Christopher; Dang, Chinh; Garcia-Lopez, Raquel; Martinez-Ferre, Almudena; Pombero, Ana; Rubenstein, John L.R.; Wakeman, Wayne B.; Hohmann, John; Dee, Nick; Sodt, Andrew J.; Young, Rob; Smith, Kimberly; Nguyen, Thuc-Nghi; Kidney, Jolene; Kuan, Leonard; Jeromin, Andreas; Kaykas, Ajamete; Miller, Jeremy; Page, Damon; Orta, Geri; Bernard, Amy; Riley, Zackery; Smith, Simon; Wohnoutka, Paul; Hawrylycz, Mike; Puelles, Luis; Jones, Allan R.

    2015-01-01

    SUMMARY To provide a temporal framework for the genoarchitecture of brain development, in situ hybridization data were generated for embryonic and postnatal mouse brain at 7 developmental stages for ~2100 genes, processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, 7 reference atlases, an ontogenetic ontology, and tools to explore co-expression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (developingmouse.brain-map.org). PMID:24952961

  14. Disease-Specific Probabilistic Brain Atlases.

    PubMed

    Thompson, Paul; Mega, Michael S; Toga, Arthur W

    2000-06-11

    Atlases of the human brain, in health and disease, provide a comprehensive framework for understanding brain structure and function. The complexity and variability of brain structure, especially in the gyral patterns of the human cortex, present challenges in creating standardized brain atlases that reflect the anatomy of a population. This paper introduces the concept of a population-based, disease-specific brain atlas that can reflect the unique anatomy and physiology of a particular clinical subpopulation. Based on well-characterized patient groups, disease-specific atlases contain thousands of structure models, composite maps, average templates, and visualizations of structural variability, asymmetry and group-specific differences. They correlate the structural, metabolic, molecular and histologic hallmarks of the disease. Rather than simply fusing information from multiple subjects and sources, new mathematical strategies are introduced to resolve group-specific features not apparent in individual scans. High-dimensional elastic mappings, based on covariant partial differential equations, are developed to encode patterns of cortical variation. In the resulting brain atlas, disease-specific features and regional asymmetries emerge that are not apparent in individual anatomies. The resulting probabilistic atlas can identify patterns of altered structure and function, and can guide algorithms for knowledge-based image analysis, automated image labeling, tissue classification, data mining and functional image analysis. PMID:19424457

  15. Disease-Specific Probabilistic Brain Atlases

    PubMed Central

    Thompson, Paul; Mega, Michael S.; Toga, Arthur W.

    2009-01-01

    Atlases of the human brain, in health and disease, provide a comprehensive framework for understanding brain structure and function. The complexity and variability of brain structure, especially in the gyral patterns of the human cortex, present challenges in creating standardized brain atlases that reflect the anatomy of a population. This paper introduces the concept of a population-based, disease-specific brain atlas that can reflect the unique anatomy and physiology of a particular clinical subpopulation. Based on well-characterized patient groups, disease-specific atlases contain thousands of structure models, composite maps, average templates, and visualizations of structural variability, asymmetry and group-specific differences. They correlate the structural, metabolic, molecular and histologic hallmarks of the disease. Rather than simply fusing information from multiple subjects and sources, new mathematical strategies are introduced to resolve group-specific features not apparent in individual scans. High-dimensional elastic mappings, based on covariant partial differential equations, are developed to encode patterns of cortical variation. In the resulting brain atlas, disease-specific features and regional asymmetries emerge that are not apparent in individual anatomies. The resulting probabilistic atlas can identify patterns of altered structure and function, and can guide algorithms for knowledge-based image analysis, automated image labeling, tissue classification, data mining and functional image analysis. PMID:19424457

  16. A Digital Atlas of the Dog Brain

    PubMed Central

    Datta, Ritobrato; Lee, Jongho; Duda, Jeffrey; Avants, Brian B.; Vite, Charles H.; Tseng, Ben; Gee, James C.; Aguirre, Gustavo D.; Aguirre, Geoffrey K.

    2012-01-01

    There is a long history and a growing interest in the canine as a subject of study in neuroscience research and in translational neurology. In the last few years, anatomical and functional magnetic resonance imaging (MRI) studies of awake and anesthetized dogs have been reported. Such efforts can be enhanced by a population atlas of canine brain anatomy to implement group analyses. Here we present a canine brain atlas derived as the diffeomorphic average of a population of fifteen mesaticephalic dogs. The atlas includes: 1) A brain template derived from in-vivo, T1-weighted imaging at 1 mm isotropic resolution at 3 Tesla (with and without the soft tissues of the head); 2) A co-registered, high-resolution (0.33 mm isotropic) template created from imaging of ex-vivo brains at 7 Tesla; 3) A surface representation of the gray matter/white matter boundary of the high-resolution atlas (including labeling of gyral and sulcal features). The properties of the atlas are considered in relation to historical nomenclature and the evolutionary taxonomy of the Canini tribe. The atlas is available for download (https://cfn.upenn.edu/aguirre/wiki/public:data_plosone_2012_datta). PMID:23284904

  17. The Scalable Brain Atlas: Instant Web-Based Access to Public Brain Atlases and Related Content.

    PubMed

    Bakker, Rembrandt; Tiesinga, Paul; Kötter, Rolf

    2015-07-01

    The Scalable Brain Atlas (SBA) is a collection of web services that provide unified access to a large collection of brain atlas templates for different species. Its main component is an atlas viewer that displays brain atlas data as a stack of slices in which stereotaxic coordinates and brain regions can be selected. These are subsequently used to launch web queries to resources that require coordinates or region names as input. It supports plugins which run inside the viewer and respond when a new slice, coordinate or region is selected. It contains 20 atlas templates in six species, and plugins to compute coordinate transformations, display anatomical connectivity and fiducial points, and retrieve properties, descriptions, definitions and 3d reconstructions of brain regions. The ambition of SBA is to provide a unified representation of all publicly available brain atlases directly in the web browser, while remaining a responsive and light weight resource that specializes in atlas comparisons, searches, coordinate transformations and interactive displays. PMID:25682754

  18. Practical MRI atlas of neonatal brain development

    SciTech Connect

    Barkovich, A.J.; Truwit, C.L.

    1990-01-01

    This book is an anatomical reference for cranial magnetic resonance imaging (MRI) studies in neonates and infants. It contains 122 clear, sharp MRI scans and drawings showing changes in the normal appearance of the brain and skull during development. Sections of the atlas depict the major processes of maturation: brain myelination, development of the corpus callosum, development of the cranial bone marrow, and iron deposition in the brain. High-quality scans illustrate how these changes appear on magnetic resonance images during various stages of development.

  19. New deformable human brain atlas for computer-aided diagnosis

    NASA Astrophysics Data System (ADS)

    Lahtinen, Antti J.; Frey, Harry; Eskola, Hannu

    2002-05-01

    Modern software-based image analysis techniques enable accurate detection of the size and shape of various brain lesions. In order to estimate the real load caused by the lesions also their neuro-anatomical location should be taken into account. Therefore deformable brain atlases appear to be essential tools when new image diagnostics methods are developed and tested. We have developed deformable brain atlas software for research and diagnosis. The atlas is used to compare patient brain images with a segmented reference brain image so that it is possible to identify the patient neuroanatomical structures. The atlas software comes with image processing tools for transforming CT or MR image sets into atlas- compatible volume image format. The reference image is deformed to match the patient image, and the segmented neuroanatomical regions of the atlas image can then be blended with the patient image.

  20. Atlas warping for brain morphometry

    NASA Astrophysics Data System (ADS)

    Machado, Alexei M. C.; Gee, James C.

    1998-06-01

    In this work, we describe an automated approach to morphometry based on spatial normalizations of the data, and demonstrate its application to the analysis of gender differences in the human corpus callosum. The purpose is to describe a population by a reduced and representative set of variables, from which a prior model can be constructed. Our approach is rooted in the assumption that individual anatomies can be considered as quantitative variations on a common underlying qualitative plane. We can therefore imagine that a given individual's anatomy is a warped version of some referential anatomy, also known as an atlas. The spatial warps which transform a labeled atlas into anatomic alignment with a population yield immediate knowledge about organ size and shape in the group. Furthermore, variation within the set of spatial warps is directly related to the anatomic variation among the subjects. Specifically, the shape statistics--mean and variance of the mappings--for the population can be calculated in a special basis, and an eigendecomposition of the variance performed to identify the most significant modes of shape variation. The results obtained with the corpus callosum study confirm the existence of substantial anatomical differences between males and females, as reported in previous experimental work.

  1. The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture.

    PubMed

    Fan, Lingzhong; Li, Hai; Zhuo, Junjie; Zhang, Yu; Wang, Jiaojian; Chen, Liangfu; Yang, Zhengyi; Chu, Congying; Xie, Sangma; Laird, Angela R; Fox, Peter T; Eickhoff, Simon B; Yu, Chunshui; Jiang, Tianzi

    2016-08-01

    The human brain atlases that allow correlating brain anatomy with psychological and cognitive functions are in transition from ex vivo histology-based printed atlases to digital brain maps providing multimodal in vivo information. Many current human brain atlases cover only specific structures, lack fine-grained parcellations, and fail to provide functionally important connectivity information. Using noninvasive multimodal neuroimaging techniques, we designed a connectivity-based parcellation framework that identifies the subdivisions of the entire human brain, revealing the in vivo connectivity architecture. The resulting human Brainnetome Atlas, with 210 cortical and 36 subcortical subregions, provides a fine-grained, cross-validated atlas and contains information on both anatomical and functional connections. Additionally, we further mapped the delineated structures to mental processes by reference to the BrainMap database. It thus provides an objective and stable starting point from which to explore the complex relationships between structure, connectivity, and function, and eventually improves understanding of how the human brain works. The human Brainnetome Atlas will be made freely available for download at http://atlas.brainnetome.org, so that whole brain parcellations, connections, and functional data will be readily available for researchers to use in their investigations into healthy and pathological states. PMID:27230218

  2. The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture

    PubMed Central

    Fan, Lingzhong; Li, Hai; Zhuo, Junjie; Zhang, Yu; Wang, Jiaojian; Chen, Liangfu; Yang, Zhengyi; Chu, Congying; Xie, Sangma; Laird, Angela R.; Fox, Peter T.; Eickhoff, Simon B.; Yu, Chunshui; Jiang, Tianzi

    2016-01-01

    The human brain atlases that allow correlating brain anatomy with psychological and cognitive functions are in transition from ex vivo histology-based printed atlases to digital brain maps providing multimodal in vivo information. Many current human brain atlases cover only specific structures, lack fine-grained parcellations, and fail to provide functionally important connectivity information. Using noninvasive multimodal neuroimaging techniques, we designed a connectivity-based parcellation framework that identifies the subdivisions of the entire human brain, revealing the in vivo connectivity architecture. The resulting human Brainnetome Atlas, with 210 cortical and 36 subcortical subregions, provides a fine-grained, cross-validated atlas and contains information on both anatomical and functional connections. Additionally, we further mapped the delineated structures to mental processes by reference to the BrainMap database. It thus provides an objective and stable starting point from which to explore the complex relationships between structure, connectivity, and function, and eventually improves understanding of how the human brain works. The human Brainnetome Atlas will be made freely available for download at http://atlas.brainnetome.org, so that whole brain parcellations, connections, and functional data will be readily available for researchers to use in their investigations into healthy and pathological states. PMID:27230218

  3. Evaluation of atlas based mouse brain segmentation

    NASA Astrophysics Data System (ADS)

    Lee, Joohwi; Jomier, Julien; Aylward, Stephen; Tyszka, Mike; Moy, Sheryl; Lauder, Jean; Styner, Martin

    2009-02-01

    Magentic Reasonance Imaging for mouse phenotype study is one of the important tools to understand human diseases. In this paper, we present a fully automatic pipeline for the process of morphometric mouse brain analysis. The method is based on atlas-based tissue and regional segmentation, which was originally developed for the human brain. To evaluate our method, we conduct a qualitative and quantitative validation study as well as compare of b-spline and fluid registration methods as components in the pipeline. The validation study includes visual inspection, shape and volumetric measurements and stability of the registration methods against various parameter settings in the processing pipeline. The result shows both fluid and b-spline registration methods work well in murine settings, but the fluid registration is more stable. Additionally, we evaluated our segmentation methods by comparing volume differences between Fmr1 FXS in FVB background vs C57BL/6J mouse strains.

  4. Large scale digital atlases in neuroscience

    NASA Astrophysics Data System (ADS)

    Hawrylycz, M.; Feng, D.; Lau, C.; Kuan, C.; Miller, J.; Dang, C.; Ng, L.

    2014-03-01

    Imaging in neuroscience has revolutionized our current understanding of brain structure, architecture and increasingly its function. Many characteristics of morphology, cell type, and neuronal circuitry have been elucidated through methods of neuroimaging. Combining this data in a meaningful, standardized, and accessible manner is the scope and goal of the digital brain atlas. Digital brain atlases are used today in neuroscience to characterize the spatial organization of neuronal structures, for planning and guidance during neurosurgery, and as a reference for interpreting other data modalities such as gene expression and connectivity data. The field of digital atlases is extensive and in addition to atlases of the human includes high quality brain atlases of the mouse, rat, rhesus macaque, and other model organisms. Using techniques based on histology, structural and functional magnetic resonance imaging as well as gene expression data, modern digital atlases use probabilistic and multimodal techniques, as well as sophisticated visualization software to form an integrated product. Toward this goal, brain atlases form a common coordinate framework for summarizing, accessing, and organizing this knowledge and will undoubtedly remain a key technology in neuroscience in the future. Since the development of its flagship project of a genome wide image-based atlas of the mouse brain, the Allen Institute for Brain Science has used imaging as a primary data modality for many of its large scale atlas projects. We present an overview of Allen Institute digital atlases in neuroscience, with a focus on the challenges and opportunities for image processing and computation.

  5. The SRI24 Multi-Channel Brain Atlas

    PubMed Central

    Rohlfing, Torsten; Zahr, Natalie M.; Sullivan, Edith V.; Pfefferbaum, Adolf

    2009-01-01

    We present a new standard atlas of the human brain based on magnetic resonance images. The atlas was generated using unbiased population registration from high-resolution images obtained by multichannel-coil acquisition at 3T in a group of 24 normal subjects. The final atlas comprises three anatomical channels (T1-weighted, early and late spin echo), three diffusion-related channels (fractional anisotropy, mean diffusivity, diffusion-weighted image), and three tissue probability maps (CSF, gray matter, white matter). The atlas is dynamic in that it is implicitly represented by nonrigid transformations between the 24 subject images, as well as distortion-correction alignments between the image channels in each subject. The atlas can, therefore, be generated at essentially arbitrary image resolutions and orientations (e.g., AC/PC aligned), without compounding interpolation artifacts. We demonstrate in this paper two different applications of the atlas: (a) region definition by label propagation in a fiber tracking study is enabled by the increased sharpness of our atlas compared with other available atlases, and (b) spatial normalization is enabled by its average shape property. In summary, our atlas has unique features and will be made available to the scientific community as a resource and reference system for future imaging-based studies of the human brain. PMID:19183706

  6. The SRI24 multichannel brain atlas: construction and applications

    NASA Astrophysics Data System (ADS)

    Rohlfing, Torsten; Zahr, Natalie M.; Sullivan, Edith V.; Pfefferbaum, Adolf

    2008-03-01

    We present a new standard atlas of the human brain based on magnetic resonance images. The atlas was generated using unbiased population registration from high-resolution images obtained by multichannel-coil acquisition at 3T in a group of 24 normal subjects. The final atlas comprises three anatomical channels (T I-weighted, early and late spin echo), three diffusion-related channels (fractional anisotropy, mean diffusivity, diffusion-weighted image), and three tissue probability maps (CSF, gray matter, white matter). The atlas is dynamic in that it is implicitly represented by nonrigid transformations between the 24 subject images, as well as distortion-correction alignments between the image channels in each subject. The atlas can, therefore, be generated at essentially arbitrary image resolutions and orientations (e.g., AC/PC aligned), without compounding interpolation artifacts. We demonstrate in this paper two different applications of the atlas: (a) region definition by label propagation in a fiber tracking study is enabled by the increased sharpness of our atlas compared with other available atlases, and (b) spatial normalization is enabled by its average shape property. In summary, our atlas has unique features and will be made available to the scientific community as a resource and reference system for future imaging-based studies of the human brain.

  7. A three-dimensional digital atlas of the starling brain.

    PubMed

    De Groof, Geert; George, Isabelle; Touj, Sara; Stacho, Martin; Jonckers, Elisabeth; Cousillas, Hugo; Hausberger, Martine; Güntürkün, Onur; Van der Linden, Annemie

    2016-05-01

    Because of their sophisticated vocal behaviour, their social nature, their high plasticity and their robustness, starlings have become an important model species that is widely used in studies of neuroethology of song production and perception. Since magnetic resonance imaging (MRI) represents an increasingly relevant tool for comparative neuroscience, a 3D MRI-based atlas of the starling brain becomes essential. Using multiple imaging protocols we delineated several sensory systems as well as the song control system. This starling brain atlas can easily be used to determine the stereotactic location of identified neural structures at any angle of the head. Additionally, the atlas is useful to find the optimal angle of sectioning for slice experiments, stereotactic injections and electrophysiological recordings. The starling brain atlas is freely available for the scientific community. PMID:25690327

  8. Development and Implementation of a Corriedale Ovine Brain Atlas for Use in Atlas-Based Segmentation

    PubMed Central

    Steward, Christopher; Moffat, Bradford Armstrong; Opie, Nicholas Lachlan; Rind, Gil Simon; John, Sam Emmanuel; Ronayne, Stephen; May, Clive Newton; O’Brien, Terence John; Milne, Marjorie Eileen; Oxley, Thomas James

    2016-01-01

    Segmentation is the process of partitioning an image into subdivisions and can be applied to medical images to isolate anatomical or pathological areas for further analysis. This process can be done manually or automated by the use of image processing computer packages. Atlas-based segmentation automates this process by the use of a pre-labelled template and a registration algorithm. We developed an ovine brain atlas that can be used as a model for neurological conditions such as Parkinson’s disease and focal epilepsy. 17 female Corriedale ovine brains were imaged in-vivo in a 1.5T (low-resolution) MRI scanner. 13 of the low-resolution images were combined using a template construction algorithm to form a low-resolution template. The template was labelled to form an atlas and tested by comparing manual with atlas-based segmentations against the remaining four low-resolution images. The comparisons were in the form of similarity metrics used in previous segmentation research. Dice Similarity Coefficients were utilised to determine the degree of overlap between eight independent, manual and atlas-based segmentations, with values ranging from 0 (no overlap) to 1 (complete overlap). For 7 of these 8 segmented areas, we achieved a Dice Similarity Coefficient of 0.5–0.8. The amygdala was difficult to segment due to its variable location and similar intensity to surrounding tissues resulting in Dice Coefficients of 0.0–0.2. We developed a low resolution ovine brain atlas with eight clinically relevant areas labelled. This brain atlas performed comparably to prior human atlases described in the literature and to intra-observer error providing an atlas that can be used to guide further research using ovine brains as a model and is hosted online for public access. PMID:27285947

  9. Development and Implementation of a Corriedale Ovine Brain Atlas for Use in Atlas-Based Segmentation.

    PubMed

    Liyanage, Kishan Andre; Steward, Christopher; Moffat, Bradford Armstrong; Opie, Nicholas Lachlan; Rind, Gil Simon; John, Sam Emmanuel; Ronayne, Stephen; May, Clive Newton; O'Brien, Terence John; Milne, Marjorie Eileen; Oxley, Thomas James

    2016-01-01

    Segmentation is the process of partitioning an image into subdivisions and can be applied to medical images to isolate anatomical or pathological areas for further analysis. This process can be done manually or automated by the use of image processing computer packages. Atlas-based segmentation automates this process by the use of a pre-labelled template and a registration algorithm. We developed an ovine brain atlas that can be used as a model for neurological conditions such as Parkinson's disease and focal epilepsy. 17 female Corriedale ovine brains were imaged in-vivo in a 1.5T (low-resolution) MRI scanner. 13 of the low-resolution images were combined using a template construction algorithm to form a low-resolution template. The template was labelled to form an atlas and tested by comparing manual with atlas-based segmentations against the remaining four low-resolution images. The comparisons were in the form of similarity metrics used in previous segmentation research. Dice Similarity Coefficients were utilised to determine the degree of overlap between eight independent, manual and atlas-based segmentations, with values ranging from 0 (no overlap) to 1 (complete overlap). For 7 of these 8 segmented areas, we achieved a Dice Similarity Coefficient of 0.5-0.8. The amygdala was difficult to segment due to its variable location and similar intensity to surrounding tissues resulting in Dice Coefficients of 0.0-0.2. We developed a low resolution ovine brain atlas with eight clinically relevant areas labelled. This brain atlas performed comparably to prior human atlases described in the literature and to intra-observer error providing an atlas that can be used to guide further research using ovine brains as a model and is hosted online for public access. PMID:27285947

  10. Whole-brain activity mapping onto a zebrafish brain atlas.

    PubMed

    Randlett, Owen; Wee, Caroline L; Naumann, Eva A; Nnaemeka, Onyeka; Schoppik, David; Fitzgerald, James E; Portugues, Ruben; Lacoste, Alix M B; Riegler, Clemens; Engert, Florian; Schier, Alexander F

    2015-11-01

    In order to localize the neural circuits involved in generating behaviors, it is necessary to assign activity onto anatomical maps of the nervous system. Using brain registration across hundreds of larval zebrafish, we have built an expandable open-source atlas containing molecular labels and definitions of anatomical regions, the Z-Brain. Using this platform and immunohistochemical detection of phosphorylated extracellular signal–regulated kinase (ERK) as a readout of neural activity, we have developed a system to create and contextualize whole-brain maps of stimulus- and behavior-dependent neural activity. This mitogen-activated protein kinase (MAP)-mapping assay is technically simple, and data analysis is completely automated. Because MAP-mapping is performed on freely swimming fish, it is applicable to studies of nearly any stimulus or behavior. Here we demonstrate our high-throughput approach using pharmacological, visual and noxious stimuli, as well as hunting and feeding. The resultant maps outline hundreds of areas associated with behaviors. PMID:26778924

  11. Whole-brain activity mapping onto a zebrafish brain atlas

    PubMed Central

    Randlett, Owen; Wee, Caroline L.; Naumann, Eva A.; Nnaemeka, Onyeka; Schoppik, David; Fitzgerald, James E.; Portugues, Ruben; Lacoste, Alix M.B.; Riegler, Clemens; Engert, Florian; Schier, Alexander F.

    2015-01-01

    In order to localize the neural circuits involved in generating behaviors, it is necessary to assign activity onto anatomical maps of the nervous system. Using brain registration across hundreds of larval zebrafish, we have built an expandable open source atlas containing molecular labels and anatomical region definitions, the Z-Brain. Using this platform and immunohistochemical detection of phosphorylated-Extracellular signal-regulated kinase (ERK/MAPK) as a readout of neural activity, we have developed a system to create and contextualize whole brain maps of stimulus- and behavior-dependent neural activity. This MAP-Mapping (Mitogen Activated Protein kinase – Mapping) assay is technically simple, fast, inexpensive, and data analysis is completely automated. Since MAP-Mapping is performed on fish that are freely swimming, it is applicable to nearly any stimulus or behavior. We demonstrate the utility of our high-throughput approach using hunting/feeding, pharmacological, visual and noxious stimuli. The resultant maps outline hundreds of areas associated with behaviors. PMID:26778924

  12. Development of MRI-based atlases of non-human brains.

    PubMed

    Ullmann, Jeremy F P; Janke, Andrew L; Reutens, David; Watson, Charles

    2015-02-15

    Brain atlases are a fundamental resource for neuroscience research. In the past few decades they have undergone a transition from traditional printed histological atlases to digital atlases made up of multiple data sets from multiple modalities, and atlases based on magnetic resonance imaging (MRI) have become widespread. Here we discuss the methods involved in making an MRI brain atlas, including registration of multiple data sets into a model, ontological classification, segmentation of a minimum deformation model, dissemination strategies, and applications of these atlases. Finally, we discuss possible future directions in the development of brain atlases. PMID:25236843

  13. Waxholm Space atlas of the Sprague Dawley rat brain.

    PubMed

    Papp, Eszter A; Leergaard, Trygve B; Calabrese, Evan; Johnson, G Allan; Bjaalie, Jan G

    2014-08-15

    Three-dimensional digital brain atlases represent an important new generation of neuroinformatics tools for understanding complex brain anatomy, assigning location to experimental data, and planning of experiments. We have acquired a microscopic resolution isotropic MRI and DTI atlasing template for the Sprague Dawley rat brain with 39 μm isotropic voxels for the MRI volume and 78 μm isotropic voxels for the DTI. Building on this template, we have delineated 76 major anatomical structures in the brain. Delineation criteria are provided for each structure. We have applied a spatial reference system based on internal brain landmarks according to the Waxholm Space standard, previously developed for the mouse brain, and furthermore connected this spatial reference system to the widely used stereotaxic coordinate system by identifying cranial sutures and related stereotaxic landmarks in the template using contrast given by the active staining technique applied to the tissue. With the release of the present atlasing template and anatomical delineations, we provide a new tool for spatial orientation analysis of neuroanatomical location, and planning and guidance of experimental procedures in the rat brain. The use of Waxholm Space and related infrastructures will connect the atlas to interoperable resources and services for multi-level data integration and analysis across reference spaces. PMID:24726336

  14. Combining Multi-atlas Segmentation with Brain Surface Estimation

    PubMed Central

    Carass, Aaron; Resnick, Susan M.; Pham, Dzung L.; Prince, Jerry L.; Landman, Bennett A.

    2016-01-01

    Whole brain segmentation (with comprehensive cortical and subcortical labels) and cortical surface reconstruction are two essential techniques for investigating the human brain. The two tasks are typically conducted independently, however, which leads to spatial inconsistencies and hinders further integrated cortical analyses. To obtain self-consistent whole brain segmentations and surfaces, FreeSurfer segregates the subcortical and cortical segmentations before and after the cortical surface reconstruction. However, this “segmentation to surface to parcellation” strategy has shown limitations in various situations. In this work, we propose a novel “multi-atlas segmentation to surface” method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. To our knowledge, this is the first work that achieves the reliability of state-of-the-art multi-atlas segmentation and labeling methods together with accurate and consistent cortical surface reconstruction. Compared with previous methods, MaCRUISE has three features: (1) MaCRUISE obtains 132 cortical/subcortical labels simultaneously from a single multi-atlas segmentation before reconstructing volume consistent surfaces; (2) Fuzzy tissue memberships are combined with multi-atlas segmentations to address partial volume effects; (3) MaCRUISE reconstructs topologically consistent cortical surfaces by using the sulci locations from multi-atlas segmentation. Two data sets, one consisting of five subjects with expertly traced landmarks and the other consisting of 100 volumes from elderly subjects are used for validation. Compared with CRUISE, MaCRUISE achieves self-consistent whole brain segmentation and cortical reconstruction without compromising on surface accuracy. MaCRUISE is comparably accurate to FreeSurfer while achieving greater robustness across an elderly

  15. Combining multi-atlas segmentation with brain surface estimation

    NASA Astrophysics Data System (ADS)

    Huo, Yuankai; Carass, Aaron; Resnick, Susan M.; Pham, Dzung L.; Prince, Jerry L.; Landman, Bennett A.

    2016-03-01

    Whole brain segmentation (with comprehensive cortical and subcortical labels) and cortical surface reconstruction are two essential techniques for investigating the human brain. The two tasks are typically conducted independently, however, which leads to spatial inconsistencies and hinders further integrated cortical analyses. To obtain self-consistent whole brain segmentations and surfaces, FreeSurfer segregates the subcortical and cortical segmentations before and after the cortical surface reconstruction. However, this "segmentation to surface to parcellation" strategy has shown limitation in various situations. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. To our knowledge, this is the first work that achieves the reliability of state-of-the-art multi-atlas segmentation and labeling methods together with accurate and consistent cortical surface reconstruction. Compared with previous methods, MaCRUISE has three features: (1) MaCRUISE obtains 132 cortical/subcortical labels simultaneously from a single multi-atlas segmentation before reconstructing volume consistent surfaces; (2) Fuzzy tissue memberships are combined with multi-atlas segmentations to address partial volume effects; (3) MaCRUISE reconstructs topologically consistent cortical surfaces by using the sulci locations from multi-atlas segmentation. Two data sets, one consisting of five subjects with expertly traced landmarks and the other consisting of 100 volumes from elderly subjects are used for validation. Compared with CRUISE, MaCRUISE achieves self-consistent whole brain segmentation and cortical reconstruction without compromising on surface accuracy. MaCRUISE is comparably accurate to FreeSurfer while achieving greater robustness across an elderly population.

  16. A computerized brain atlas: construction, anatomical content, and some applications.

    PubMed

    Greitz, T; Bohm, C; Holte, S; Eriksson, L

    1991-01-01

    An adjustable computerized atlas of the human brain has been developed, which can be adapted to fit individual anatomy. It is primarily intended for positron emission tomography (PET) but may also be used for single photon emission CT, transmission CT, magnetic resonance imaging, and neuroimaging-based procedures, such as stereotactic surgery and radiotherapy. The atlas is based on anatomical information obtained from brains fixed in situ soon after death. All structures have been drawn in on digitized photos of slices from one cryosectioned brain. The definition and classification of the anatomical structures and divisions are in agreement with the standard textbooks of anatomy, and the nomenclature is that of the Nomina Anatomica of 1965. The boundaries of the cortical cytoarchitectonic areas (Brodmann areas) have been determined using information from several sources, since three-dimensional literature data on their distribution are incomplete, scarce, and partly contradictory. However, no analysis of the cytoarchitectonics of the atlas brain itself has been undertaken. At present the data base contains three-dimensional representations of the brain surface, the ventricular system, the cortical gyri and sulci, as well as the Brodmann cytoarchitectonic areas. The major basal ganglia, the brain stem nuclei, the lobuli of the vermis, and the cerebellar hemispheres are also included. The computerized atlas can be used to improve the quantification and evaluation of PET data in several ways. For instance, it can serve as a guide in selecting regions of interest. It may also facilitate comparisons of data from different individuals or groups of individuals, by applying the inverse atlas transformation to PET data volume, thus relating the PET information to the anatomy of the reference atlas rather than to the patient's anatomy. Reformatted PET data from individuals can thus be averaged, and averages from different categories or different functional states of patients

  17. Construction of brain atlases based on a multi-center MRI dataset of 2020 Chinese adults.

    PubMed

    Liang, Peipeng; Shi, Lin; Chen, Nan; Luo, Yishan; Wang, Xing; Liu, Kai; Mok, Vincent C T; Chu, Winnie C W; Wang, Defeng; Li, Kuncheng

    2015-01-01

    Despite the known morphological differences (e.g., brain shape and size) in the brains of populations of different origins (e.g., age and race), the Chinese brain atlas is less studied. In the current study, we developed a statistical brain atlas based on a multi-center high quality magnetic resonance imaging (MRI) dataset of 2020 Chinese adults (18-76 years old). We constructed 12 Chinese brain atlas from the age 20 year to the age 75 at a 5 years interval. New Chinese brain standard space, coordinates, and brain area labels were further defined. The new Chinese brain atlas was validated in brain registration and segmentation. It was found that, as contrast to the MNI152 template, the proposed Chinese atlas showed higher accuracy in hippocampus segmentation and relatively smaller shape deformations during registration. These results indicate that a population-specific time varying brain atlas may be more appropriate for studies involving Chinese populations. PMID:26678304

  18. Transformations and algorithms in a computerized brain atlas

    SciTech Connect

    Thurfjell, L. . Centre for Image Analysis); Bohm, C. . Dept. of Physics); Eriksson, L. . Dept. of Neuroradiology Karolinska Institute/Hospital, Stockholm . Dept of Clinical Neurophysiology)

    1993-08-01

    The computerized brain atlas constructed at the Karolinska Hospital, Stockholm, Sweden, has been further developed. This atlas was designed to be employed in different fields of neuro imaging such as positron emission tomography (PET), single photon emission tomography (SPECT), computerized tomography (CT) and magnetic resonance imaging (MR). The main objectives with the atlas is to aid the interpretation of functional images by introducing anatomical information, to serve as a tool in the merging of data from different imaging modalities and to facilitate the comparisons of data from different individuals by allowing for anatomical standardization of individual data. The purpose of this paper is to describe the algorithms and transformations used in the implementation of the atlas software.

  19. Atlas-Guided Segmentation of Vervet Monkey Brain MRI

    PubMed Central

    Fedorov, Andriy; Li, Xiaoxing; Pohl, Kilian M; Bouix, Sylvain; Styner, Martin; Addicott, Merideth; Wyatt, Chris; Daunais, James B; Wells, William M; Kikinis, Ron

    2011-01-01

    The vervet monkey is an important nonhuman primate model that allows the study of isolated environmental factors in a controlled environment. Analysis of monkey MRI often suffers from lower quality images compared with human MRI because clinical equipment is typically used to image the smaller monkey brain and higher spatial resolution is required. This, together with the anatomical differences of the monkey brains, complicates the use of neuroimage analysis pipelines tuned for human MRI analysis. In this paper we developed an open source image analysis framework based on the tools available within the 3D Slicer software to support a biological study that investigates the effect of chronic ethanol exposure on brain morphometry in a longitudinally followed population of male vervets. We first developed a computerized atlas of vervet monkey brain MRI, which was used to encode the typical appearance of the individual brain structures in MRI and their spatial distribution. The atlas was then used as a spatial prior during automatic segmentation to process two longitudinal scans per subject. Our evaluation confirms the consistency and reliability of the automatic segmentation. The comparison of atlas construction strategies reveals that the use of a population-specific atlas leads to improved accuracy of the segmentation for subcortical brain structures. The contribution of this work is twofold. First, we describe an image processing workflow specifically tuned towards the analysis of vervet MRI that consists solely of the open source software tools. Second, we develop a digital atlas of vervet monkey brain MRIs to enable similar studies that rely on the vervet model. PMID:22253661

  20. Stereotactic PET atlas of the human brain: Aid for visual interpretation of functional brain images

    SciTech Connect

    Minoshima, S.; Koeppe, R.A.; Frey, A.; Ishihara, M.; Kuhl, D.E.

    1994-06-01

    In the routine analysis of functional brain images obtained by PET, subjective visual interpretation is often used for anatomic localization. To enhance the accuracy and consistency of the anatomic interpretation, a PET stereotactic atlas and localization approach was designed for functional brain images. The PET atlas was constructed from a high-resolution [{sup 18}F]fluorodeoxyglucose (FDG) image set of a normal volunteer (a 41-yr-ld woman). The image set was reoriented stereotactically, according to the intercommissural (anterior and posterior commissures) line and transformed to the standard stereotactic atlas coordinates. Cerebral structures were annotated on the transaxial planes using a proportional grid system and surface-rendered images. The stereotactic localization technique was applied to image sets from patients with Alzheimer`s disease, and areas of functional alteration were localized visually by referring to the PET atlas. Major brain structures were identified on both transaxial planes and surface-rendered images. In the stereotactic system, anatomic correspondence between the PET atlas and stereotactically reoriented individual image sets of patients with Alzheimer`s disease facilitated both indirect and direct localization of the cerebral structures. Because rapid stereotactic alignment methods for PET images are now available for routine use, the PET atlas will serve as an aid for visual interpretation of functional brain images in the stereotactic system. Widespread application of stereotactic localization may be used in functional brain images, not only in the research setting, but also in routine clinical situations. 41 refs., 3 figs.

  1. The Brain Atlas Concordance Problem: Quantitative Comparison of Anatomical Parcellations

    PubMed Central

    Bohland, Jason W.; Bokil, Hemant; Allen, Cara B.; Mitra, Partha P.

    2009-01-01

    Many neuroscientific reports reference discrete macro-anatomical regions of the brain which were delineated according to a brain atlas or parcellation protocol. Currently, however, no widely accepted standards exist for partitioning the cortex and subcortical structures, or for assigning labels to the resulting regions, and many procedures are being actively used. Previous attempts to reconcile neuroanatomical nomenclatures have been largely qualitative, focusing on the development of thesauri or simple semantic mappings between terms. Here we take a fundamentally different approach, discounting the names of regions and instead comparing their definitions as spatial entities in an effort to provide more precise quantitative mappings between anatomical entities as defined by different atlases. We develop an analytical framework for studying this brain atlas concordance problem, and apply these methods in a comparison of eight diverse labeling methods used by the neuroimaging community. These analyses result in conditional probabilities that enable mapping between regions across atlases, which also form the input to graph-based methods for extracting higher-order relationships between sets of regions and to procedures for assessing the global similarity between different parcellations of the same brain. At a global scale, the overall results demonstrate a considerable lack of concordance between available parcellation schemes, falling within chance levels for some atlas pairs. At a finer level, this study reveals spatial relationships between sets of defined regions that are not obviously apparent; these are of high potential interest to researchers faced with the challenge of comparing results that were based on these different anatomical models, particularly when coordinate-based data are not available. The complexity of the spatial overlap patterns revealed points to problems for attempts to reconcile anatomical parcellations and nomenclatures using strictly

  2. Consistent cortical reconstruction and multi-atlas brain segmentation.

    PubMed

    Huo, Yuankai; Plassard, Andrew J; Carass, Aaron; Resnick, Susan M; Pham, Dzung L; Prince, Jerry L; Landman, Bennett A

    2016-09-01

    Whole brain segmentation and cortical surface reconstruction are two essential techniques for investigating the human brain. Spatial inconsistences, which can hinder further integrated analyses of brain structure, can result due to these two tasks typically being conducted independently of each other. FreeSurfer obtains self-consistent whole brain segmentations and cortical surfaces. It starts with subcortical segmentation, then carries out cortical surface reconstruction, and ends with cortical segmentation and labeling. However, this "segmentation to surface to parcellation" strategy has shown limitations in various cohorts such as older populations with large ventricles. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. A modification called MaCRUISE(+) is designed to perform well when white matter lesions are present. Comparing to the benchmarks CRUISE and FreeSurfer, the surface accuracy of MaCRUISE and MaCRUISE(+) is validated using two independent datasets with expertly placed cortical landmarks. A third independent dataset with expertly delineated volumetric labels is employed to compare segmentation performance. Finally, 200MR volumetric images from an older adult sample are used to assess the robustness of MaCRUISE and FreeSurfer. The advantages of MaCRUISE are: (1) MaCRUISE constructs self-consistent voxelwise segmentations and cortical surfaces, while MaCRUISE(+) is robust to white matter pathology. (2) MaCRUISE achieves more accurate whole brain segmentations than independently conducting the multi-atlas segmentation. (3) MaCRUISE is comparable in accuracy to FreeSurfer (when FreeSurfer does not exhibit global failures) while achieving greater robustness across an older adult population. MaCRUISE has been made freely

  3. A three-dimensional digital atlas of the zebrafish brain.

    PubMed

    Ullmann, Jeremy F P; Cowin, Gary; Kurniawan, Nyoman D; Collin, Shaun P

    2010-05-15

    In the past three decades, the zebrafish has become a vital animal model in a range of biological sciences. To augment current neurobiological research, we have developed the first three-dimensional digital atlas of the zebrafish brain from T2-weighted magnetic resonance histology (MRH) images acquired on a 16.4-T superconducting magnet. We achieved an isotropic resolution of 10 microm, which is the highest resolution achieved in a vertebrate brain and, for the first time, is comparable in slice thickness to conventional histology. By using manual segmentation, 53 anatomical structures, including fiber tracts as small as 40 microm, were delineated. Using Amira software, structures were also individually segmented and reconstructed to create three-dimensional animations. Additional quantitative information including, volume, surface areas, and mean gray scale intensities were also determined. Finally, we established a stereotaxic coordinate system as a framework in which maps created from other modalities can be incorporated into the atlas. PMID:20139016

  4. Windows on the brain: the emerging role of atlases and databases in neuroscience

    NASA Technical Reports Server (NTRS)

    Van Essen, David C.; VanEssen, D. C. (Principal Investigator)

    2002-01-01

    Brain atlases and associated databases have great potential as gateways for navigating, accessing, and visualizing a wide range of neuroscientific data. Recent progress towards realizing this potential includes the establishment of probabilistic atlases, surface-based atlases and associated databases, combined with improvements in visualization capabilities and internet access.

  5. Digital Atlas of the Zebra Finch (Taeniopygia guttata) Brain: a High Resolution Photo Atlas

    PubMed Central

    Karten, Harvey J.; Brzozowska-Prechtl, Agnieszka; Lovell, Peter V.; Tang, Daniel D.; Mello, Claudio V.; Wang, Haibin; Mitra, Partha P.

    2014-01-01

    We describe a set of new comprehensive, high-quality, high-resolution digital images of histological sections from the brain of male zebra finches (Taeniopygia guttata), and make them publicly available through an interactive website (http://zebrafinch.brainarchitecture.org/). These images provide a basis for the production of a dimensionally accurate and detailed digital non-stereotaxic atlas. Nissl- and myelin-stained brain sections are provided in the transverse, sagittal, and horizontal planes, with the transverse plane approximating the more traditional Frankfurt Plane. In addition, a separate set of brain sections in this same plane is stained for tyrosine hydroxylase, revealing the distribution of catecholaminergic neurons (dopaminergic, noradrenergic, and adrenergic) in the songbird brain. For a subset of sagittal sections we have also prepared a corresponding set of drawings, defining and annotating various nuclei, fields, and fiber tracts that are visible under Nissl and myelin staining. This atlas of the zebra finch brain is expected to become an important tool for birdsong research and comparative studies of brain organization and evolution. PMID:23896990

  6. High-resolution in vivo Wistar rodent brain atlas based on T1 weighted image

    NASA Astrophysics Data System (ADS)

    Huang, Su; Lu, Zhongkang; Huang, Weimin; Seramani, Sankar; Ramasamy, Boominathan; Sekar, Sakthivel; Guan, Cuntai; Bhakoo, Kishore

    2016-03-01

    Image based atlases for rats brain have a significant impact on pre-clinical research. In this project we acquired T1-weighted images from Wistar rodent brains with fine 59μm isotropical resolution for generation of the atlas template image. By applying post-process procedures using a semi-automatic brain extraction method, we delineated the brain tissues from source data. Furthermore, we applied a symmetric group-wise normalization method to generate an optimized template of T1 image of rodent brain, then aligned our template to the Waxholm Space. In addition, we defined several simple and explicit landmarks to corresponding our template with the well known Paxinos stereotaxic reference system. Anchoring at the origin of the Waxholm Space, we applied piece-wise linear transformation method to map the voxels of the template into the coordinates system in Paxinos' stereotoxic coordinates to facilitate the labelling task. We also cross-referenced our data with both published rodent brain atlas and image atlases available online, methodologically labelling the template to produce a Wistar brain atlas identifying more than 130 structures. Particular attention was paid to the cortex and cerebellum, as these areas encompass the most researched aspects of brain functions. Moreover, we adopted the structure hierarchy and naming nomenclature common to various atlases, so that the names and hierarchy structure presented in the atlas are readily recognised for easy use. It is believed the atlas will present a useful tool in rodent brain functional and pharmaceutical studies.

  7. Tumor growth model for atlas based registration of pathological brain MR images

    NASA Astrophysics Data System (ADS)

    Moualhi, Wafa; Ezzeddine, Zagrouba

    2015-02-01

    The motivation of this work is to register a tumor brain magnetic resonance (MR) image with a normal brain atlas. A normal brain atlas is deformed in order to take account of the presence of a large space occupying tumor. The method use a priori model of tumor growth assuming that the tumor grows in a radial way from a starting point. First, an affine transformation is used in order to bring the patient image and the brain atlas in a global correspondence. Second, the seeding of a synthetic tumor into the brain atlas provides a template for the lesion. Finally, the seeded atlas is deformed combining a method derived from optical flow principles and a model for tumor growth (MTG). Results show that an automatic segmentation method of brain structures in the presence of large deformation can be provided.

  8. Detail-preserving construction of neonatal brain atlases in space-frequency domain.

    PubMed

    Zhang, Yuyao; Shi, Feng; Yap, Pew-Thian; Shen, Dinggang

    2016-06-01

    Brain atlases are commonly utilized in neuroimaging studies. However, most brain atlases are fuzzy and lack structural details, especially in the cortical regions. This is mainly caused by the image averaging process involved in atlas construction, which often smoothes out high-frequency contents that capture fine anatomical details. Brain atlas construction for neonatal images is even more challenging due to insufficient spatial resolution and low tissue contrast. In this paper, we propose a novel framework for detail-preserving construction of population-representative atlases. Our approach combines spatial and frequency information to better preserve image details. This is achieved by performing atlas construction in the space-frequency domain given by wavelet transform. In particular, sparse patch-based atlas construction is performed in all frequency subbands, and the results are combined to give a final atlas. For enhancing anatomical details, tissue probability maps are also used to guide atlas construction. Experimental results show that our approach can produce atlases with greater structural details than existing atlases. Hum Brain Mapp 37:2133-2150, 2016. © 2016 Wiley Periodicals, Inc. PMID:26987787

  9. A pediatric brain structure atlas from T1-weighted MR images

    NASA Astrophysics Data System (ADS)

    Shan, Zuyao Y.; Parra, Carlos; Ji, Qing; Ogg, Robert J.; Zhang, Yong; Laningham, Fred H.; Reddick, Wilburn E.

    2006-03-01

    In this paper, we have developed a digital atlas of the pediatric human brain. Human brain atlases, used to visualize spatially complex structures of the brain, are indispensable tools in model-based segmentation and quantitative analysis of brain structures. However, adult brain atlases do not adequately represent the normal maturational patterns of the pediatric brain, and the use of an adult model in pediatric studies may introduce substantial bias. Therefore, we proposed to develop a digital atlas of the pediatric human brain in this study. The atlas was constructed from T1 weighted MR data set of a 9 year old, right-handed girl. Furthermore, we extracted and simplified boundary surfaces of 25 manually defined brain structures (cortical and subcortical) based on surface curvature. Higher curvature surfaces were simplified with more reference points; lower curvature surfaces, with fewer. We constructed a 3D triangular mesh model for each structure by triangulation of the structure's reference points. Kappa statistics (cortical, 0.97; subcortical, 0.91) indicated substantial similarities between the mesh-defined and the original volumes. Our brain atlas and structural mesh models (www.stjude.org/BrainAtlas) can be used to plan treatment, to conduct knowledge and modeldriven segmentation, and to analyze the shapes of brain structures in pediatric patients.

  10. Automatic segmentation and classification of human brain image based on a fuzzy brain atlas

    NASA Astrophysics Data System (ADS)

    Tan, Ou; Jia, Chunguang; Duan, Huilong; Lu, Weixue

    1998-09-01

    It is difficult to automatically segment and classify tomograph images of actual patient's brain. Therefore, many interactive operations are performed. It is very time consuming and its precision is much depended on the user. In this paper, we combine a brain atlas and 3D fuzzy image segmentation into the image matching. It can not only find out the precise boundary of anatomic structure but also save time of the interactive operation. At first, the anatomic information of atlas is mapped into tomograph images of actual brain with a two step image matching method. Then, based on the mapping result, a 3D fuzzy structure mask is calculated. With the fuzzy information of anatomic structure, a new method of fuzzy clustering based on genetic algorithm is used to segment and classify the real brain image. There is only a minimum requirement of interaction in the whole process, including removing the skull and selecting some intrinsic point pairs.

  11. Quantitative analysis of brain pathology based on MRI and brain atlases--applications for cerebral palsy.

    PubMed

    Faria, Andreia V; Hoon, Alexander; Stashinko, Elaine; Li, Xin; Jiang, Hangyi; Mashayekh, Ameneh; Akhter, Kazi; Hsu, John; Oishi, Kenichi; Zhang, Jiangyang; Miller, Michael I; van Zijl, Peter C M; Mori, Susumu

    2011-02-01

    We have developed a new method to provide a comprehensive quantitative analysis of brain anatomy in cerebral palsy patients, which makes use of two techniques: diffusion tensor imaging and automated 3D whole brain segmentation based on our brain atlas and a nonlinear normalization technique (large-deformation diffeomorphic metric mapping). This method was applied to 13 patients and normal controls. The reliability of the automated segmentation revealed close agreement with the manual segmentation. We illustrate some potential applications for individual characterization and group comparison. This technique also provides a framework for determining the impact of various neuroanatomic features on brain functions. PMID:20920589

  12. Quantitative Analysis of Brain Pathology Based on MRI and Brain Atlases - Applications for Cerebral Palsy

    PubMed Central

    Faria, Andreia V.; Hoon, Alexander; Stachinko, Elaine; Li, Xin; Jiang, Hangyi; Mashayekh, Ameneh; Akhter, Kazi; Hsu, John; Oishi, Kenichi; Zhang, Jiangyang; Miller, Michael I.; van Zijl, Peter C.M.; Mori, Susumu

    2010-01-01

    We have developed a new method to provide a comprehensive quantitative analysis of brain anatomy in cerebral palsy patients, which makes use of two techniques: diffusion tensor imaging and automated 3D whole brain segmentation based on our brain atlas and a nonlinear normalization technique (large-deformation diffeomorphic metric mapping). This method was applied to 13 patients and normal controls. The reliability of the automated segmentation revealed close agreement with the manual segmentation. We illustrate some potential applications for individual characterization and group comparison. This technique also provides a framework for determining the impact of various neuroanatomic features on brain functions. PMID:20920589

  13. An Open-Source Label Atlas Correction Tool and Preliminary Results on Huntingtons Disease Whole-Brain MRI Atlases

    PubMed Central

    Forbes, Jessica L.; Kim, Regina E. Y.; Paulsen, Jane S.; Johnson, Hans J.

    2016-01-01

    The creation of high-quality medical imaging reference atlas datasets with consistent dense anatomical region labels is a challenging task. Reference atlases have many uses in medical image applications and are essential components of atlas-based segmentation tools commonly used for producing personalized anatomical measurements for individual subjects. The process of manual identification of anatomical regions by experts is regarded as a so-called gold standard; however, it is usually impractical because of the labor-intensive costs. Further, as the number of regions of interest increases, these manually created atlases often contain many small inconsistently labeled or disconnected regions that need to be identified and corrected. This project proposes an efficient process to drastically reduce the time necessary for manual revision in order to improve atlas label quality. We introduce the LabelAtlasEditor tool, a SimpleITK-based open-source label atlas correction tool distributed within the image visualization software 3D Slicer. LabelAtlasEditor incorporates several 3D Slicer widgets into one consistent interface and provides label-specific correction tools, allowing for rapid identification, navigation, and modification of the small, disconnected erroneous labels within an atlas. The technical details for the implementation and performance of LabelAtlasEditor are demonstrated using an application of improving a set of 20 Huntingtons Disease-specific multi-modal brain atlases. Additionally, we present the advantages and limitations of automatic atlas correction. After the correction of atlas inconsistencies and small, disconnected regions, the number of unidentified voxels for each dataset was reduced on average by 68.48%. PMID:27536233

  14. An Open-Source Label Atlas Correction Tool and Preliminary Results on Huntingtons Disease Whole-Brain MRI Atlases.

    PubMed

    Forbes, Jessica L; Kim, Regina E Y; Paulsen, Jane S; Johnson, Hans J

    2016-01-01

    The creation of high-quality medical imaging reference atlas datasets with consistent dense anatomical region labels is a challenging task. Reference atlases have many uses in medical image applications and are essential components of atlas-based segmentation tools commonly used for producing personalized anatomical measurements for individual subjects. The process of manual identification of anatomical regions by experts is regarded as a so-called gold standard; however, it is usually impractical because of the labor-intensive costs. Further, as the number of regions of interest increases, these manually created atlases often contain many small inconsistently labeled or disconnected regions that need to be identified and corrected. This project proposes an efficient process to drastically reduce the time necessary for manual revision in order to improve atlas label quality. We introduce the LabelAtlasEditor tool, a SimpleITK-based open-source label atlas correction tool distributed within the image visualization software 3D Slicer. LabelAtlasEditor incorporates several 3D Slicer widgets into one consistent interface and provides label-specific correction tools, allowing for rapid identification, navigation, and modification of the small, disconnected erroneous labels within an atlas. The technical details for the implementation and performance of LabelAtlasEditor are demonstrated using an application of improving a set of 20 Huntingtons Disease-specific multi-modal brain atlases. Additionally, we present the advantages and limitations of automatic atlas correction. After the correction of atlas inconsistencies and small, disconnected regions, the number of unidentified voxels for each dataset was reduced on average by 68.48%. PMID:27536233

  15. Interactive brain atlas with the Visible Human Project data: development methods and techniques.

    PubMed

    Toh, M Y; Falk, R B; Main, J S

    1996-09-01

    A prototype of an interactive digital brain atlas was developed by using the Visible Human Project data set of the National Library of Medicine. This data set provides corresponding axial magnetic resonance images, computed tomographic images, and cryosections of the brain. The prototype was developed to demonstrate the techniques and methods that will be used throughout the development process of the atlas. The atlas has a graphical user interface, supports user interaction with various representations of the brain (i.e., two-dimensional and three-dimensional [3D]), and displays multiple images simultaneously. Motion sequences of the 3D brain were incorporated in the atlas to provide an important link between two-dimensional brain slices and volume-rendered 3D anatomic structures. Volume visualization tools were used to interactively render, rotate, and reslice the volumetric brain data. The brain was segmented with manual tracing, thresholding, and morphologic algorithms and then rendered with volume-rendering tools. PMID:8888399

  16. Regional growth and atlasing of the developing human brain

    PubMed Central

    Makropoulos, Antonios; Aljabar, Paul; Wright, Robert; Hüning, Britta; Merchant, Nazakat; Arichi, Tomoki; Tusor, Nora; Hajnal, Joseph V.; Edwards, A. David; Counsell, Serena J.; Rueckert, Daniel

    2016-01-01

    Detailed morphometric analysis of the neonatal brain is required to characterise brain development and define neuroimaging biomarkers related to impaired brain growth. Accurate automatic segmentation of neonatal brain MRI is a prerequisite to analyse large datasets. We have previously presented an accurate and robust automatic segmentation technique for parcellating the neonatal brain into multiple cortical and subcortical regions. In this study, we further extend our segmentation method to detect cortical sulci and provide a detailed delineation of the cortical ribbon. These detailed segmentations are used to build a 4-dimensional spatio-temporal structural atlas of the brain for 82 cortical and subcortical structures throughout this developmental period. We employ the algorithm to segment an extensive database of 420 MR images of the developing brain, from 27 to 45 weeks post-menstrual age at imaging. Regional volumetric and cortical surface measurements are derived and used to investigate brain growth and development during this critical period and to assess the impact of immaturity at birth. Whole brain volume, the absolute volume of all structures studied, cortical curvature and cortical surface area increased with increasing age at scan. Relative volumes of cortical grey matter, cerebellum and cerebrospinal fluid increased with age at scan, while relative volumes of white matter, ventricles, brainstem and basal ganglia and thalami decreased. Preterm infants at term had smaller whole brain volumes, reduced regional white matter and cortical and subcortical grey matter volumes, and reduced cortical surface area compared with term born controls, while ventricular volume was greater in the preterm group. Increasing prematurity at birth was associated with a reduction in total and regional white matter, cortical and subcortical grey matter volume, an increase in ventricular volume, and reduced cortical surface area. PMID:26499811

  17. Regional growth and atlasing of the developing human brain.

    PubMed

    Makropoulos, Antonios; Aljabar, Paul; Wright, Robert; Hüning, Britta; Merchant, Nazakat; Arichi, Tomoki; Tusor, Nora; Hajnal, Joseph V; Edwards, A David; Counsell, Serena J; Rueckert, Daniel

    2016-01-15

    Detailed morphometric analysis of the neonatal brain is required to characterise brain development and define neuroimaging biomarkers related to impaired brain growth. Accurate automatic segmentation of neonatal brain MRI is a prerequisite to analyse large datasets. We have previously presented an accurate and robust automatic segmentation technique for parcellating the neonatal brain into multiple cortical and subcortical regions. In this study, we further extend our segmentation method to detect cortical sulci and provide a detailed delineation of the cortical ribbon. These detailed segmentations are used to build a 4-dimensional spatio-temporal structural atlas of the brain for 82 cortical and subcortical structures throughout this developmental period. We employ the algorithm to segment an extensive database of 420 MR images of the developing brain, from 27 to 45weeks post-menstrual age at imaging. Regional volumetric and cortical surface measurements are derived and used to investigate brain growth and development during this critical period and to assess the impact of immaturity at birth. Whole brain volume, the absolute volume of all structures studied, cortical curvature and cortical surface area increased with increasing age at scan. Relative volumes of cortical grey matter, cerebellum and cerebrospinal fluid increased with age at scan, while relative volumes of white matter, ventricles, brainstem and basal ganglia and thalami decreased. Preterm infants at term had smaller whole brain volumes, reduced regional white matter and cortical and subcortical grey matter volumes, and reduced cortical surface area compared with term born controls, while ventricular volume was greater in the preterm group. Increasing prematurity at birth was associated with a reduction in total and regional white matter, cortical and subcortical grey matter volume, an increase in ventricular volume, and reduced cortical surface area. PMID:26499811

  18. 3D brain atlas reconstructor service--online repository of three-dimensional models of brain structures.

    PubMed

    Majka, Piotr; Kowalski, Jakub M; Chlodzinska, Natalia; Wójcik, Daniel K

    2013-10-01

    Brain atlases are important tools of neuroscience. Traditionally prepared in paper book format, more and more commonly they take digital form which extends their utility. To simplify work with different atlases, to lay the ground for developing universal tools which could abstract from the origin of the atlas, efforts are being made to provide common interfaces to these atlases. 3D Brain Atlas Reconstructor service (3dBARs) described here is a repository of digital representations of different brain atlases in CAF format which we recently proposed and a repository of 3D models of brain structures. A graphical front-end is provided for creating and viewing the reconstructed models as well as the underlying 2D atlas data. An application programming interface (API) facilitates programmatic access to the service contents from other websites. From a typical user's point of view, 3dBARs offers an accessible way to mine publicly available atlasing data with a convenient browser based interface, without the need to install extra software. For a developer of services related to brain atlases, 3dBARs supplies mechanisms for enhancing functionality of other software. The policy of the service is to accept new datasets as delivered by interested parties and we work with the researchers who obtain original data to make them available to the neuroscience community at large. The functionality offered by the 3dBARs situates it at the core of present and future general atlasing services tying it strongly to the global atlasing neuroinformatics infrastructure. PMID:23943281

  19. BrainMaps.org - Interactive High-Resolution Digital Brain Atlases and Virtual Microscopy.

    PubMed

    Mikula, Shawn; Stone, James M; Jones, Edward G

    2008-01-01

    BrainMaps.org is an interactive high-resolution digital brain atlas and virtual microscope that is based on over 20 million megapixels of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet. Complete brain datasets for various species, including Homo sapiens, Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, and Tyto alba, are accessible online. The methods and tools we describe are useful for both research and teaching, and can be replicated by labs seeking to increase accessibility and sharing of neuroanatomical data. These tools offer the possibility of visualizing and exploring completely digitized sections of brains at a sub-neuronal level, and can facilitate large-scale connectional tracing, histochemical and stereological analyses. PMID:19129928

  20. A diffusion tensor MRI atlas of the postmortem rhesus macaque brain.

    PubMed

    Calabrese, Evan; Badea, Alexandra; Coe, Christopher L; Lubach, Gabriele R; Shi, Yundi; Styner, Martin A; Johnson, G Allan

    2015-08-15

    The rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate for modeling the structure and function of the brain. Brain atlases, and particularly those based on magnetic resonance imaging (MRI), have become important tools for understanding normal brain structure, and for identifying structural abnormalities resulting from disease states, exposures, and/or aging. Diffusion tensor imaging (DTI)-based MRI brain atlases are widely used in both human and macaque brain imaging studies because of the unique contrasts, quantitative diffusion metrics, and diffusion tractography that they can provide. Previous MRI and DTI atlases of the rhesus brain have been limited by low contrast and/or low spatial resolution imaging. Here we present a microscopic resolution MRI/DTI atlas of the rhesus brain based on 10 postmortem brain specimens. The atlas includes both structural MRI and DTI image data, a detailed three-dimensional segmentation of 241 anatomic structures, diffusion tractography, cortical thickness estimates, and maps of anatomic variability among atlas specimens. This atlas incorporates many useful features from previous work, including anatomic label nomenclature and ontology, data orientation, and stereotaxic reference frame, and further extends prior analyses with the inclusion of high-resolution multi-contrast image data. PMID:26037056

  1. Multi-atlas segmentation of subcortical brain structures via the AutoSeg software pipeline.

    PubMed

    Wang, Jiahui; Vachet, Clement; Rumple, Ashley; Gouttard, Sylvain; Ouziel, Clémentine; Perrot, Emilie; Du, Guangwei; Huang, Xuemei; Gerig, Guido; Styner, Martin

    2014-01-01

    Automated segmenting and labeling of individual brain anatomical regions, in MRI are challenging, due to the issue of individual structural variability. Although atlas-based segmentation has shown its potential for both tissue and structure segmentation, due to the inherent natural variability as well as disease-related changes in MR appearance, a single atlas image is often inappropriate to represent the full population of datasets processed in a given neuroimaging study. As an alternative for the case of single atlas segmentation, the use of multiple atlases alongside label fusion techniques has been introduced using a set of individual "atlases" that encompasses the expected variability in the studied population. In our study, we proposed a multi-atlas segmentation scheme with a novel graph-based atlas selection technique. We first paired and co-registered all atlases and the subject MR scans. A directed graph with edge weights based on intensity and shape similarity between all MR scans is then computed. The set of neighboring templates is selected via clustering of the graph. Finally, weighted majority voting is employed to create the final segmentation over the selected atlases. This multi-atlas segmentation scheme is used to extend a single-atlas-based segmentation toolkit entitled AutoSeg, which is an open-source, extensible C++ based software pipeline employing BatchMake for its pipeline scripting, developed at the Neuro Image Research and Analysis Laboratories of the University of North Carolina at Chapel Hill. AutoSeg performs N4 intensity inhomogeneity correction, rigid registration to a common template space, automated brain tissue classification based skull-stripping, and the multi-atlas segmentation. The multi-atlas-based AutoSeg has been evaluated on subcortical structure segmentation with a testing dataset of 20 adult brain MRI scans and 15 atlas MRI scans. The AutoSeg achieved mean Dice coefficients of 81.73% for the subcortical structures. PMID

  2. A Three-dimensional Deformable Brain Atlas for DBS Targeting. I. Methodology for Atlas Creation and Artifact Reduction

    PubMed Central

    Sudhyadhom, Atchar; Okun, Michael S; Foote, Kelly D; Rahman, Maryam; Bova, Frank J

    2012-01-01

    Background: Targeting in deep brain stimulation (DBS) relies heavily on the ability to accurately localize particular anatomic brain structures. Direct targeting of subcortical structures has been limited by the ability to visualize relevant DBS targets. Methods and Results: In this work, we describe the development and implementation, of a methodology utilized to create a three dimensional deformable atlas for DBS surgery. This atlas was designed to correspond to the print version of the Schaltenbrand-Bailey atlas structural contours. We employed a smoothing technique to reduce artifacts inherent in the print version. Conclusions: We present the methodology used to create a three dimensional patient specific DBS atlas which may in the future be tested for clinical utility. PMID:23091579

  3. Multi-atlas segmentation of subcortical brain structures via the AutoSeg software pipeline

    PubMed Central

    Wang, Jiahui; Vachet, Clement; Rumple, Ashley; Gouttard, Sylvain; Ouziel, Clémentine; Perrot, Emilie; Du, Guangwei; Huang, Xuemei; Gerig, Guido; Styner, Martin

    2014-01-01

    Automated segmenting and labeling of individual brain anatomical regions, in MRI are challenging, due to the issue of individual structural variability. Although atlas-based segmentation has shown its potential for both tissue and structure segmentation, due to the inherent natural variability as well as disease-related changes in MR appearance, a single atlas image is often inappropriate to represent the full population of datasets processed in a given neuroimaging study. As an alternative for the case of single atlas segmentation, the use of multiple atlases alongside label fusion techniques has been introduced using a set of individual “atlases” that encompasses the expected variability in the studied population. In our study, we proposed a multi-atlas segmentation scheme with a novel graph-based atlas selection technique. We first paired and co-registered all atlases and the subject MR scans. A directed graph with edge weights based on intensity and shape similarity between all MR scans is then computed. The set of neighboring templates is selected via clustering of the graph. Finally, weighted majority voting is employed to create the final segmentation over the selected atlases. This multi-atlas segmentation scheme is used to extend a single-atlas-based segmentation toolkit entitled AutoSeg, which is an open-source, extensible C++ based software pipeline employing BatchMake for its pipeline scripting, developed at the Neuro Image Research and Analysis Laboratories of the University of North Carolina at Chapel Hill. AutoSeg performs N4 intensity inhomogeneity correction, rigid registration to a common template space, automated brain tissue classification based skull-stripping, and the multi-atlas segmentation. The multi-atlas-based AutoSeg has been evaluated on subcortical structure segmentation with a testing dataset of 20 adult brain MRI scans and 15 atlas MRI scans. The AutoSeg achieved mean Dice coefficients of 81.73% for the subcortical structures

  4. A magnetic resonance image based atlas of the rabbit brain for automatic parcellation.

    PubMed

    Muñoz-Moreno, Emma; Arbat-Plana, Ariadna; Batalle, Dafnis; Soria, Guadalupe; Illa, Miriam; Prats-Galino, Alberto; Eixarch, Elisenda; Gratacos, Eduard

    2013-01-01

    Rabbit brain has been used in several works for the analysis of neurodevelopment. However, there are not specific digital rabbit brain atlases that allow an automatic identification of brain regions, which is a crucial step for various neuroimage analyses, and, instead, manual delineation of areas of interest must be performed in order to evaluate a specific structure. For this reason, we propose an atlas of the rabbit brain based on magnetic resonance imaging, including both structural and diffusion weighted, that can be used for the automatic parcellation of the rabbit brain. Ten individual atlases, as well as an average template and probabilistic maps of the anatomical regions were built. In addition, an example of automatic segmentation based on this atlas is described. PMID:23844007

  5. Space-Frequency Detail-Preserving Construction of Neonatal Brain Atlases

    PubMed Central

    Zhang, Yuyao; Shi, Feng; Yap, Pew-Thian; Shen, Dinggang

    2016-01-01

    Brain atlases are an integral component of neuroimaging studies. However, most brain atlases are fuzzy and lack structural details, especially in the cortical regions. In particular, neonatal brain atlases are especially challenging to construct due to the low spatial resolution and low tissue contrast. This is mainly caused by the image averaging process involved in atlas construction, often smoothing out high-frequency contents that indicate fine anatomical details. In this paper, we propose a novel framework for detail-preserving construction of atlases. Our approach combines space and frequency information to better preserve image details. This is achieved by performing reconstruction in the space-frequency domain given by wavelet transform. Sparse patch-based atlas reconstruction is performed in each frequency subband. Combining the results for all these subbands will then result in a refined atlas. Compared with existing atlases, experimental results indicate that our approach has the ability to build an atlas with more structural details, thus leading to better performance when used to normalize a group of testing neonatal images. PMID:27169138

  6. Population-averaged diffusion tensor imaging atlas of the Sprague Dawley rat brain.

    PubMed

    Veraart, Jelle; Leergaard, Trygve B; Antonsen, Bjørnar T; Van Hecke, Wim; Blockx, Ines; Jeurissen, Ben; Jiang, Yi; Van der Linden, Annemie; Johnson, G Allan; Verhoye, Marleen; Sijbers, Jan

    2011-10-15

    Rats are widely used in experimental neurobiological research, and rat brain atlases are important resources for identifying brain regions in the context of experimental microsurgery, tissue sampling, and neuroimaging, as well as comparison of findings across experiments. Currently, most available rat brain atlases are constructed from histological material derived from single specimens, and provide two-dimensional or three-dimensional (3D) outlines of diverse brain regions and fiber tracts. Important limitations of such atlases are that they represent individual specimens, and that finer details of tissue architecture are lacking. Access to more detailed 3D brain atlases representative of a population of animals is needed. Diffusion tensor imaging (DTI) is a unique neuroimaging modality that provides sensitive information about orientation structure in tissues, and is widely applied in basic and clinical neuroscience investigations. To facilitate analysis and assignment of location in rat brain neuroimaging investigations, we have developed a population-averaged three-dimensional DTI atlas of the normal adult Sprague Dawley rat brain. The atlas is constructed from high resolution ex vivo DTI images, which were nonlinearly warped into a population-averaged in vivo brain template. The atlas currently comprises a selection of manually delineated brain regions, the caudate-putamen complex, globus pallidus, entopeduncular nucleus, substantia nigra, external capsule, corpus callosum, internal capsule, cerebral peduncle, fimbria of the hippocampus, fornix, anterior commisure, optic tract, and stria terminalis. The atlas is freely distributed and potentially useful for several purposes, including automated and manual delineation of rat brain structural and functional imaging data. PMID:21749925

  7. Genomic connectivity networks based on the BrainSpan atlas of the developing human brain

    NASA Astrophysics Data System (ADS)

    Mahfouz, Ahmed; Ziats, Mark N.; Rennert, Owen M.; Lelieveldt, Boudewijn P. F.; Reinders, Marcel J. T.

    2014-03-01

    The human brain comprises systems of networks that span the molecular, cellular, anatomic and functional levels. Molecular studies of the developing brain have focused on elucidating networks among gene products that may drive cellular brain development by functioning together in biological pathways. On the other hand, studies of the brain connectome attempt to determine how anatomically distinct brain regions are connected to each other, either anatomically (diffusion tensor imaging) or functionally (functional MRI and EEG), and how they change over development. A global examination of the relationship between gene expression and connectivity in the developing human brain is necessary to understand how the genetic signature of different brain regions instructs connections to other regions. Furthermore, analyzing the development of connectivity networks based on the spatio-temporal dynamics of gene expression provides a new insight into the effect of neurodevelopmental disease genes on brain networks. In this work, we construct connectivity networks between brain regions based on the similarity of their gene expression signature, termed "Genomic Connectivity Networks" (GCNs). Genomic connectivity networks were constructed using data from the BrainSpan Transcriptional Atlas of the Developing Human Brain. Our goal was to understand how the genetic signatures of anatomically distinct brain regions relate to each other across development. We assessed the neurodevelopmental changes in connectivity patterns of brain regions when networks were constructed with genes implicated in the neurodevelopmental disorder autism (autism spectrum disorder; ASD). Using graph theory metrics to characterize the GCNs, we show that ASD-GCNs are relatively less connected later in development with the cerebellum showing a very distinct expression of ASD-associated genes compared to other brain regions.

  8. A customizable 3-dimensional digital atlas of the canary brain in multiple modalities.

    PubMed

    Vellema, Michiel; Verschueren, Jacob; Van Meir, Vincent; Van der Linden, Annemie

    2011-07-15

    Songbirds are well known for their ability to learn their vocalizations by imitating conspecific adults. This uncommon skill has led to many studies examining the behavioral and neurobiological processes involved in vocal learning. Canaries display a variable, seasonally dependent, vocal behavior throughout their lives. This trait makes this bird species particularly valuable to study the functional relationship between the continued plasticity in the singing behavior and alterations in the anatomy and physiology of the brain. In order to optimally interpret these types of studies, a detailed understanding of the brain anatomy is essential. Because traditional 2-dimensional brain atlases are limited in the information they can provide about the anatomy of the brain, here we present a 3-dimensional MRI-based atlas of the canary brain. Using multiple imaging protocols we were able to maximize the number of detectable brain regions, including most of the areas involved in song perception, learning, and production. The brain atlas can readily be used to determine the stereotactic location of delineated brain areas at any desirable head angle. Alternatively the brain data can be used to determine the ideal orientation of the brain for stereotactic injections, electrophysiological recordings, and brain sectioning. The 3-dimensional canary brain atlas presented here is freely available and is easily adaptable to support many types of neurobiological studies, including anatomical, electrophysiological, histological, explant, and tracer studies. PMID:21565273

  9. The SRI24 Multi-Channel Brain Atlas: Construction and Applications.

    PubMed

    Rohlfing, Torsten; Zahr, Natalie M; Sullivan, Edith V; Pfefferbaum, Adolf

    2008-01-01

    We present a new standard atlas of the human brain based on magnetic resonance images. The atlas was generated using unbiased population registration from high-resolution images obtained by multichannel-coil acquisition at 3T in a group of 24 normal subjects. The final atlas comprises three anatomical channels (T(1)-weighted, early and late spin echo), three diffusion-related channels (fractional anisotropy, mean diffusivity, diffusion-weighted image), and three tissue probability maps (CSF, gray matter, white matter). The atlas is dynamic in that it is implicitly represented by nonrigid transformations between the 24 subject images, as well as distortion-correction alignments between the image channels in each subject. The atlas can, therefore, be generated at essentially arbitrary image resolutions and orientations (e.g., AC/PC aligned), without compounding interpolation artifacts. We demonstrate in this paper two different applications of the atlas: (a) region definition by label propagation in a fiber tracking study is enabled by the increased sharpness of our atlas compared with other available atlases, and (b) spatial normalization is enabled by its average shape property. In summary, our atlas has unique features and will be made available to the scientific community as a resource and reference system for future imaging-based studies of the human brain. PMID:19183706

  10. A combined histological and MRI brain atlas of the common marmoset monkey, Callithrix jacchus

    PubMed Central

    Newman, John D.; Kenkel, William M.; Aronoff, Emily C.; Bock, Nicholas A.; Zametkin, Molly R.; Silva, Afonso C.

    2009-01-01

    The common marmoset, Callithrix jacchus, is of growing importance for research in neuroscience and related fields. In the present work, we describe a combined histological and magnetic resonance imaging (MRI) atlas constructed from the brains of two adult female marmosets. Histological sections were processed from Nissl staining and digitized to produce an atlas in a large format that facilitates visualization of structures with significant detail. Naming of identifiable brain structures was performed utilizing current terminology. The histological sections and a simplified schematic atlas are available online at http://udn.nichd.nih.gov/brainatlas_home.html. PMID:19744521

  11. The SRI24 multichannel atlas of normal adult human brain structure.

    PubMed

    Rohlfing, Torsten; Zahr, Natalie M; Sullivan, Edith V; Pfefferbaum, Adolf

    2010-05-01

    This article describes the SRI24 atlas, a new standard reference system of normal human brain anatomy, that was created using template-free population registration of high-resolution magnetic resonance images acquired at 3T in a group of 24 normal control subjects. The atlas comprises anatomical channels (T1, T2, and proton density weighted), diffusion-related channels (fractional anisotropy, mean diffusivity, longitudinal diffusivity, mean diffusion-weighted image), tissue channels (CSF probability, gray matter probability, white matter probability, tissue labels), and two cortical parcellation maps. The SRI24 atlas enables multichannel atlas-to-subject image registration. It is uniquely versatile in that it is equally suited for the two fundamentally different atlas applications: label propagation and spatial normalization. Label propagation, herein demonstrated using diffusion tensor image fiber tracking, is enabled by the increased sharpness of the SRI24 atlas compared with other available atlases. Spatial normalization, herein demonstrated using data from a young-old group comparison study, is enabled by its unbiased average population shape property. For both propagation and normalization, we also report the results of quantitative comparisons with seven other published atlases: Colin27, MNI152, ICBM452 (warp5 and air12), and LPBA40 (SPM5, FLIRT, AIR). Our results suggest that the SRI24 atlas, although based on 3T MR data, allows equally accurate spatial normalization of data acquired at 1.5T as the comparison atlases, all of which are based on 1.5T data. Furthermore, the SRI24 atlas is as suitable for label propagation as the comparison atlases and detailed enough to allow delineation of anatomical structures for this purpose directly in the atlas. PMID:20017133

  12. The SRI24 Multi-Channel Atlas of Normal Adult Human Brain Structure

    PubMed Central

    Rohlfing, Torsten; Zahr, Natalie M.; Sullivan, Edith V.; Pfefferbaum, Adolf

    2010-01-01

    This paper describes the SRI24 atlas, a new standard reference system of normal human brain anatomy, that was created using template-free population registration of high-resolution magnetic resonance images acquired at 3T in a group of 24 normal control subjects. The atlas comprises anatomical channels (T1, T2, and proton density weighted), diffusion-related channels (fractional anisotropy, mean diffusivity, longitudinal diffusivity, mean diffusion-weighted image), tissue channels (CSF probability, gray matter probability, white matter probability, tissue labels), and two cortical parcellation maps. The SRI24 atlas enables multi-channel atlas-to-subject image registration. It is uniquely versatile in that it is equally suited for the two fundamentally different atlas applications: label propagation and spatial normalization. Label propagation, herein demonstrated using DTI fiber tracking, is enabled by the increased sharpness of the SRI24 atlas compared with other available atlases. Spatial normalization, herein demonstrated using data from a young-old group comparison study, is enabled by its unbiased average population shape property. For both propagation and normalization, we also report the results of quantitative comparisons with seven other published atlases: Colin27, MNI152, ICBM452 (warp5 and air12), and LPBA40 (SPM5, FLIRT, AIR). Our results suggest that the SRI24 atlas, although based on 3T MR data, allows equally accurate spatial normalization of data acquired at 1.5T as the comparison atlases, all of which are based on 1.5T data. Furthermore, the SRI24 atlas is as suitable for label propagation as the comparison atlases and detailed enough to allow delineation of anatomical structures for this purpose directly in the atlas. PMID:20017133

  13. Atlas-based segmentation of pathological MR brain images using a model of lesion growth.

    PubMed

    Cuadra, Meritxell Bach; Pollo, Claudio; Bardera, Anton; Cuisenaire, Olivier; Villemure, Jean-Guy; Thiran, Jean-Philippe

    2004-10-01

    We propose a method for brain atlas deformation in the presence of large space-occupying tumors, based on an a priori model of lesion growth that assumes radial expansion of the lesion from its starting point. Our approach involves three steps. First, an affine registration brings the atlas and the patient into global correspondence. Then, the seeding of a synthetic tumor into the brain atlas provides a template for the lesion. The last step is the deformation of the seeded atlas, combining a method derived from optical flow principles and a model of lesion growth. Results show that a good registration is performed and that the method can be applied to automatic segmentation of structures and substructures in brains with gross deformation, with important medical applications in neurosurgery, radiosurgery, and radiotherapy. PMID:15493697

  14. Automatic tissue segmentation of neonate brain MR Images with subject-specific atlases

    NASA Astrophysics Data System (ADS)

    Cherel, Marie; Budin, Francois; Prastawa, Marcel; Gerig, Guido; Lee, Kevin; Buss, Claudia; Lyall, Amanda; Zaldarriaga Consing, Kirsten; Styner, Martin

    2015-03-01

    Automatic tissue segmentation of the neonate brain using Magnetic Resonance Images (MRI) is extremely important to study brain development and perform early diagnostics but is challenging due to high variability and inhomogeneity in contrast throughout the image due to incomplete myelination of the white matter tracts. For these reasons, current methods often totally fail or give unsatisfying results. Furthermore, most of the subcortical midbrain structures are misclassified due to a lack of contrast in these regions. We have developed a novel method that creates a probabilistic subject-specific atlas based on a population atlas currently containing a number of manually segmented cases. The generated subject-specific atlas is sharp and adapted to the subject that is being processed. We then segment brain tissue classes using the newly created atlas with a single-atlas expectation maximization based method. Our proposed method leads to a much lower failure rate in our experiments. The overall segmentation results are considerably improved when compared to using a non-subject-specific, population average atlas. Additionally, we have incorporated diffusion information obtained from Diffusion Tensor Images (DTI) to improve the detection of white matter that is not visible at this early age in structural MRI (sMRI) due to a lack of myelination. Although this necessitates the acquisition of an additional sequence, the diffusion information improves the white matter segmentation throughout the brain, especially for the mid-brain structures such as the corpus callosum and the internal capsule.

  15. Structural Brain Atlases: Design, Rationale, and Applications in Normal and Pathological Cohorts

    PubMed Central

    Mandal, Pravat K.; Mahajan, Rashima; Dinov, Ivo D.

    2015-01-01

    Structural magnetic resonance imaging (MRI) provides anatomical information about the brain in healthy as well as in diseased conditions. On the other hand, functional MRI (fMRI) provides information on the brain activity during performance of a specific task. Analysis of fMRI data requires the registration of the data to a reference brain template in order to identify the activated brain regions. Brain templates also find application in other neuroimaging modalities, such as diffusion tensor imaging and multi-voxel spectroscopy. Further, there are certain differences (e.g., brain shape and size) in the brains of populations of different origin and during diseased conditions like in Alzheimer’s disease (AD), population and disease-specific brain templates may be considered crucial for accurate registration and subsequent analysis of fMRI as well as other neuroimaging data. This manuscript provides a comprehensive review of the history, construction and application of brain atlases. A chronological outline of the development of brain template design, starting from the Talairach and Tournoux atlas to the Chinese brain template (to date), along with their respective detailed construction protocols provides the backdrop to this manuscript. The manuscript also provides the automated workflow-based protocol for designing a population-specific brain atlas from structural MRI data using LONI Pipeline graphical workflow environment. We conclude by discussing the scope of brain templates as a research tool and their application in various neuroimaging modalities. PMID:22647262

  16. Standard atlas space for C57BL/6J neonatal mouse brain.

    PubMed

    Lee, Erh-Fang; Jacobs, Russell E; Dinov, Ivo; Leow, Alex; Toga, Arthur W

    2005-11-01

    A standard atlas space with stereotaxic co-ordinates for the postnatal day 0 (P0) C57BL/6J mouse brain was constructed from the average of eight individual co-registered MR image volumes. Accuracy of registration and morphometric variations in structures between subjects were analyzed statistically. We also applied this atlas coordinate system to data acquired using different imaging protocols as well as to a high-resolution histological atlas obtained from separate animals. Mapping accuracy in the atlas space was examined to determine the applicability of this atlas framework. The results show that the atlas space defined here provides a stable framework for image registration for P0 normal mouse brains. With an appropriate feature-based co-registration strategy, the probability atlas can also provide an accurate anatomical map for images acquired using invasive imaging methods. The atlas templates and the probability map of the anatomical labels are available at http://www.loni.ucla.edu/MAP/ . PMID:16228227

  17. A Multidimensional Magnetic Resonance Histology Atlas of the Wistar Rat Brain

    PubMed Central

    Johnson, G. Allan; Calabrese, Evan; Badea, Alexandra; Paxinos, George; Watson, Charles

    2012-01-01

    We have produced a multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). This MR atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies. PMID:22634863

  18. Multiscale Exploration of Mouse Brain Microstructures Using the Knife-Edge Scanning Microscope Brain Atlas

    PubMed Central

    Chung, Ji Ryang; Sung, Chul; Mayerich, David; Kwon, Jaerock; Miller, Daniel E.; Huffman, Todd; Keyser, John; Abbott, Louise C.; Choe, Yoonsuck

    2011-01-01

    Connectomics is the study of the full connection matrix of the brain. Recent advances in high-throughput, high-resolution 3D microscopy methods have enabled the imaging of whole small animal brains at a sub-micrometer resolution, potentially opening the road to full-blown connectomics research. One of the first such instruments to achieve whole-brain-scale imaging at sub-micrometer resolution is the Knife-Edge Scanning Microscope (KESM). KESM whole-brain data sets now include Golgi (neuronal circuits), Nissl (soma distribution), and India ink (vascular networks). KESM data can contribute greatly to connectomics research, since they fill the gap between lower resolution, large volume imaging methods (such as diffusion MRI) and higher resolution, small volume methods (e.g., serial sectioning electron microscopy). Furthermore, KESM data are by their nature multiscale, ranging from the subcellular to the whole organ scale. Due to this, visualization alone is a huge challenge, before we even start worrying about quantitative connectivity analysis. To solve this issue, we developed a web-based neuroinformatics framework for efficient visualization and analysis of the multiscale KESM data sets. In this paper, we will first provide an overview of KESM, then discuss in detail the KESM data sets and the web-based neuroinformatics framework, which is called the KESM brain atlas (KESMBA). Finally, we will discuss the relevance of the KESMBA to connectomics research, and identify challenges and future directions. PMID:22275895

  19. Brain atlas of the Mongolian gerbil (Meriones unguiculatus) in CT/MRI-aided stereotaxic coordinates.

    PubMed

    Radtke-Schuller, Susanne; Schuller, Gerd; Angenstein, Frank; Grosser, Oliver S; Goldschmidt, Jürgen; Budinger, Eike

    2016-09-01

    A new stereotaxic brain atlas of the Mongolian gerbil (Meriones unguiculatus), an important animal model in neurosciences, is presented. It combines high-quality histological material for identification of brain structures with reliable stereotaxic coordinates. The atlas consists of high-resolution images of frontal sections alternately stained for cell bodies (Nissl) and myelinated fibers (Gallyas) of 62 rostro-caudal levels at intervals of 350 μm. Brain structures were named according to the Paxinos nomenclature for rodents. The accuracy of the stereotaxic coordinate system was improved substantially by comparing and matching the series of histological sections to in vivo brain images of the gerbil obtained by magnetic resonance imaging (MRI). The skull outlines corresponding to the MR images were acquired using X-ray computerized tomography (CT) and were used to establish the relationship between coordinates of brain structures and skull. Landmarks such as lambda, bregma, ear canals and occipital crest can be used to line up skull and brain in standard atlas coordinates. An easily reproducible protocol allows sectioning of experimental brains in the standard frontal plane of the atlas. PMID:27507296

  20. Usefulness of brain atlases in neuroradiology: Current status and future potential.

    PubMed

    Nowinski, Wieslaw L

    2016-08-01

    Human brain atlases, although prevalent in medical education and stereotactic and functional neurosurgery, are not yet applied practically in neuroradiology. In a step towards introducing brain atlases to neuroradiology, we discuss nine different situations of potential atlas use: (1) to support interpretation of brain scans with clearly visible structures (to increase confidence of non-neuroradiologists); (2) to delineate and label scans of low anatomical content (with indiscernible or poorly visible anatomy); (3) to assist in generating the structured report; (4) to assist in interpreting small deep lesions, since an atlas's anatomical parcellation is higher than that of the interpreted scan; (5) to approximate distorted due to pathology (and unknown to the interpreter) anatomy and label it; (6) to cope with data explosion; (7) to assist in the interpretation of functional scans (to label the activation foci with the underlying anatomy and Brodmann's areas); (8) to support ischemic stroke image handling by means of atlases of anatomy and blood supply territories; and (9) to communicate image interpretation results (diagnosis) to others. The usefulness of the atlas for automatic structure identification, localisation, delineation, labelling and quantification, as well as for reporting and communication, potentially increases the interpreter's efficiency and confidence, as well as expedites image interpretation. PMID:27154190

  1. 3-Dimensional Diffusion Tensor Imaging (DTI) Atlas of the Rat Brain

    PubMed Central

    Rumple, Ashley; McMurray, Matthew; Johns, Josephine; Lauder, Jean; Makam, Pooja; Radcliffe, Marlana; Oguz, Ipek

    2013-01-01

    Anatomical atlases play an important role in the analysis of neuroimaging data in rodent neuroimaging studies. Having a high resolution, detailed atlas not only can expand understanding of rodent brain anatomy, but also enables automatic segmentation of new images, thus greatly increasing the efficiency of future analysis when applied to new data. These atlases can be used to analyze new scans of individual cases using a variety of automated segmentation methods. This project seeks to develop a set of detailed 3D anatomical atlases of the brain at postnatal day 5 (P5), 14 (P14), and adults (P72) in Sprague-Dawley rats. Our methods consisted of first creating a template image based on fixed scans of control rats, then manually segmenting various individual brain regions on the template. Using itk-SNAP software, subcortical and cortical regions, including both white matter and gray matter structures, were manually segmented in the axial, sagittal, and coronal planes. The P5, P14, and P72 atlases had 39, 45, and 29 regions segmented, respectively. These atlases have been made available to the broader research community. PMID:23861758

  2. Atlas-based segmentation of deep brain structures using non-rigid registration

    NASA Astrophysics Data System (ADS)

    Khan, Muhammad Faisal; Mewes, Klaus; Gross, Robert E.; Škrinjar, Oskar

    2008-03-01

    Deep brain structures are frequently used as targets in neurosurgical procedures. However, the boundaries of these structures are often not visible in clinically used MR and CT images. Techniques based on anatomical atlases and indirect targeting are used to infer the location of these targets intraoperatively. Initial errors of such approaches may be up to a few millimeters, which is not negligible. E.g. subthalamic nucleus is approximately 4x6 mm in the axial plane and the diameter of globus pallidus internus is approximately 8 mm, both of which are used as targets in deep brain stimulation surgery. To increase the initial localization accuracy of deep brain structures we have developed an atlas-based segmentation method that can be used for the surgery planning. The atlas is a high resolution MR head scan of a healthy volunteer with nine deep brain structures manually segmented. The quality of the atlas image allowed for the segmentation of the deep brain structures, which is not possible from the clinical MR head scans of patients. The subject image is non-rigidly registered to the atlas image using thin plate splines to represent the transformation and normalized mutual information as a similarity measure. The obtained transformation is used to map the segmented structures from the atlas to the subject image. We tested the approach on five subjects. The quality of the atlas-based segmentation was evaluated by visual inspection of the third and lateral ventricles, putamena, and caudate nuclei, which are visible in the subject MR images. The agreement of these structures for the five tested subjects was approximately 1 to 2 mm.

  3. High-resolution digital brain atlases: a Hubble telescope for the brain.

    PubMed

    Jones, Edward G; Stone, James M; Karten, Harvey J

    2011-05-01

    We describe implementation of a method for digitizing at microscopic resolution brain tissue sections containing normal and experimental data and for making the content readily accessible online. Web-accessible brain atlases and virtual microscopes for online examination can be developed using existing computer and internet technologies. Resulting databases, made up of hierarchically organized, multiresolution images, enable rapid, seamless navigation through the vast image datasets generated by high-resolution scanning. Tools for visualization and annotation of virtual microscope slides enable remote and universal data sharing. Interactive visualization of a complete series of brain sections digitized at subneuronal levels of resolution offers fine grain and large-scale localization and quantification of many aspects of neural organization and structure. The method is straightforward and replicable; it can increase accessibility and facilitate sharing of neuroanatomical data. It provides an opportunity for capturing and preserving irreplaceable, archival neurohistological collections and making them available to all scientists in perpetuity, if resources could be obtained from hitherto uninterested agencies of scientific support. PMID:21599693

  4. A Web-based Brain Atlas of the Vervet Monkey, Chlorocebus aethiops

    PubMed Central

    Woods, Roger P.; Fears, Scott C.; Jorgensen, Matthew J.; Fairbanks, Lynn A.; Toga, Arthur W.; Freimer, Nelson B.

    2010-01-01

    Vervet monkeys are a frequently studied animal model in neuroscience research. Although equally distantly related to humans, the ancestors of vervets diverged from those of macaques and baboons more than eleven million years ago, antedating the divergence of the ancestors of humans, chimpanzees and gorillas. To facilitate anatomic localization in the vervet brain, two linked on-line electronic atlases are described, one based on registered MRI scans from hundreds of vervets (http://www.loni.ucla.edu/Research/Atlases/Data/vervet/vervetmratlas/vervetmratlas.html) and the other based on a high-resolution cryomacrotome study of a single vervet (http://www.loni.ucla.edu/Research/Atlases/Data/vervet/vervetatlas/vervetatlas.html). The averaged MRI atlas is also available as a volume in Neuroimaging Informatics Technology Initiative format. In the cryomacrotome atlas, various sulcal and subcortical structures have been anatomically labeled and surface rendered views are provided along the primary planes of section. Both atlases simultaneously provide views in all three primary planes of section, rapid navigation by clicking on the displayed images, and stereotaxic coordinates in the averaged MRI atlas space. Despite the extended time period since their divergence, the major sulcal and subcortical landmarks in vervets are highly conserved relative to those described in macaques. PMID:20923706

  5. Use of Brain MRI Atlases to Determine Boundaries of Age-Related Pathology: The Importance of Statistical Method

    PubMed Central

    Dickie, David Alexander; Job, Dominic E.; Gonzalez, David Rodriguez; Shenkin, Susan D.; Wardlaw, Joanna M.

    2015-01-01

    Introduction Neurodegenerative disease diagnoses may be supported by the comparison of an individual patient’s brain magnetic resonance image (MRI) with a voxel-based atlas of normal brain MRI. Most current brain MRI atlases are of young to middle-aged adults and parametric, e.g., mean ±standard deviation (SD); these atlases require data to be Gaussian. Brain MRI data, e.g., grey matter (GM) proportion images, from normal older subjects are apparently not Gaussian. We created a nonparametric and a parametric atlas of the normal limits of GM proportions in older subjects and compared their classifications of GM proportions in Alzheimer’s disease (AD) patients. Methods Using publicly available brain MRI from 138 normal subjects and 138 subjects diagnosed with AD (all 55–90 years), we created: a mean ±SD atlas to estimate parametrically the percentile ranks and limits of normal ageing GM; and, separately, a nonparametric, rank order-based GM atlas from the same normal ageing subjects. GM images from AD patients were then classified with respect to each atlas to determine the effect statistical distributions had on classifications of proportions of GM in AD patients. Results The parametric atlas often defined the lower normal limit of the proportion of GM to be negative (which does not make sense physiologically as the lowest possible proportion is zero). Because of this, for approximately half of the AD subjects, 25–45% of voxels were classified as normal when compared to the parametric atlas; but were classified as abnormal when compared to the nonparametric atlas. These voxels were mainly concentrated in the frontal and occipital lobes. Discussion To our knowledge, we have presented the first nonparametric brain MRI atlas. In conditions where there is increasing variability in brain structure, such as in old age, nonparametric brain MRI atlases may represent the limits of normal brain structure more accurately than parametric approaches. Therefore, we

  6. A Unified Framework for Cross-modality Multi-atlas Segmentation of Brain MRI

    PubMed Central

    Iglesias, Juan Eugenio; Sabuncu, Mert Rory; Leemput, Koen Van

    2013-01-01

    Multi-atlas label fusion is a powerful image segmentation strategy that is becoming increasingly popular in medical imaging. A standard label fusion algorithm relies on independently computed pairwise registrations between individual atlases and the (target) image to be segmented. These registrations are then used to propagate the atlas labels to the target space and fuse them into a single final segmentation. Such label fusion schemes commonly rely on the similarity between intensity values of the atlases and target scan, which is often problematic in medical imaging - in particular, when the atlases and target images are obtained via different sensor types or imaging protocols. In this paper, we present a generative probabilistic model that yields an algorithm for solving the atlas-to-target registrations and label fusion steps simultaneously. The proposed model does not directly rely on the similarity of image intensities. Instead, it exploits the consistency of voxel intensities within the target scan to drive the registration and label fusion, hence the atlases and target image can be of different modalities. Furthermore, the framework models the joint warp of all the atlases, introducing interdependence between the registrations. We use variational expectation maximization and the Demons registration framework in order to efficiently identify the most probable segmentation and registrations. We use two sets of experiments to illustrate the approach, where proton density (PD) MRI atlases are used to segment T1-weighted brain scans and vice versa. Our results clearly demonstrate the accuracy gain due to exploiting within-target intensity consistency and integrating registration into label fusion. PMID:24001931

  7. A unified framework for cross-modality multi-atlas segmentation of brain MRI.

    PubMed

    Eugenio Iglesias, Juan; Rory Sabuncu, Mert; Van Leemput, Koen

    2013-12-01

    Multi-atlas label fusion is a powerful image segmentation strategy that is becoming increasingly popular in medical imaging. A standard label fusion algorithm relies on independently computed pairwise registrations between individual atlases and the (target) image to be segmented. These registrations are then used to propagate the atlas labels to the target space and fuse them into a single final segmentation. Such label fusion schemes commonly rely on the similarity between intensity values of the atlases and target scan, which is often problematic in medical imaging - in particular, when the atlases and target images are obtained via different sensor types or imaging protocols. In this paper, we present a generative probabilistic model that yields an algorithm for solving the atlas-to-target registrations and label fusion steps simultaneously. The proposed model does not directly rely on the similarity of image intensities. Instead, it exploits the consistency of voxel intensities within the target scan to drive the registration and label fusion, hence the atlases and target image can be of different modalities. Furthermore, the framework models the joint warp of all the atlases, introducing interdependence between the registrations. We use variational expectation maximization and the Demons registration framework in order to efficiently identify the most probable segmentation and registrations. We use two sets of experiments to illustrate the approach, where proton density (PD) MRI atlases are used to segment T1-weighted brain scans and vice versa. Our results clearly demonstrate the accuracy gain due to exploiting within-target intensity consistency and integrating registration into label fusion. PMID:24001931

  8. The construction of a Chinese MRI brain atlas: a morphometric comparison study between Chinese and Caucasian cohorts.

    PubMed

    Tang, Yuchun; Hojatkashani, Cornelius; Dinov, Ivo D; Sun, Bo; Fan, Lingzhong; Lin, Xiangtao; Qi, Hengtao; Hua, Xue; Liu, Shuwei; Toga, Arthur W

    2010-05-15

    We developed a novel brain atlas template to facilitate computational brain studies of Chinese subjects and populations using high quality magnetic resonance imaging (MRI) and well-validated image analysis techniques. To explore the ethnicity-based structural brain differences, we used the MRI scans of 35 Chinese male subjects (24.03+/-2.06 years) and compared them to an age-matched cohort of 35 Caucasian males (24.03+/-2.06 years). Global volumetric measures were used to identify significant group differences in the brain length, width, height and AC-PC line distance. Using the LONI BrainParser, 56 brain structures were automatically labeled and analyzed for all subjects. We identified significant ethnicity differences in brain structure volumes, suggesting that a population-specific brain atlas may be more appropriate for studies involving Chinese populations. To address this, we constructed a 3D Chinese brain atlas based on high resolution 3.0T MRI scans of 56 right-handed male Chinese volunteers (24.46+/-1.81 years). All Chinese brains were spatially normalized by using linear and nonlinear transformation via the "AIR Make Atlas" pipeline workflow within the LONI pipeline environment. This high-resolution Chinese brain atlas was compared to the ICBM152 template, which was constructed using Caucasian brains. PMID:20152910

  9. The human brain in 1700 pieces: design and development of a three-dimensional, interactive and reference atlas.

    PubMed

    Nowinski, W L; Chua, B C; Qian, G Y; Nowinska, N G

    2012-02-15

    As the human brain is the most complex living organ, constructing its detailed model with exploration capabilities in a form of an atlas is a challenge. Our overall goal is to construct an advanced, detailed, parcellated, labeled, accurate, interactive, three-dimensional (3D), and scalable whole human brain atlas of structure, vasculature, tracts and systems. The objectives of this work are three-fold; to present: (1) method of atlas design and development including design principles, accuracy requirements, atlas content, architecture, functionality, user interface, and customized tools; (2) creation of an atlas of structure and systems including its modeling method and validation; and (3) integration of this atlas with the cerebrovasculature and tracts created earlier. The atlas is created from multiple in vivo 3/7 T scans. Its design based on "pyramidal principle" enables scalability while preserving design principles and exploits interaction paradigm "from blocks to brain". The atlas contains (1) navigator with modules for system/object/object state management, interaction, user interfacing, and rendering; and (2) brain model with cerebrum, cerebellum, brainstem, spinal cord, white matter, deep structures, systems, ventricles, arteries, veins, sinuses, and tracts. The brain model is parcellated, labeled, consistent, realistic, of high resolution, polygonal/volumetric, dissectible, extendable, and deformable. It has over 1700 3D components. The atlas has sub-voxel accuracy of 0.1mm and the smallest vessels of 80 μm. Brain exploration includes dynamic scene composition, manipulation-independent 3D labeling, interaction combined with animation, meta-labeling, and quantification. This atlas is useful in education, research, and clinical applications. It can potentially be foundation for a multi-level molecular-cellular-anatomical-physiological-behavioral platform. PMID:22062451

  10. Parcellation of the Healthy Neonatal Brain into 107 Regions Using Atlas Propagation through Intermediate Time Points in Childhood.

    PubMed

    Blesa, Manuel; Serag, Ahmed; Wilkinson, Alastair G; Anblagan, Devasuda; Telford, Emma J; Pataky, Rozalia; Sparrow, Sarah A; Macnaught, Gillian; Semple, Scott I; Bastin, Mark E; Boardman, James P

    2016-01-01

    Neuroimage analysis pipelines rely on parcellated atlases generated from healthy individuals to provide anatomic context to structural and diffusion MRI data. Atlases constructed using adult data introduce bias into studies of early brain development. We aimed to create a neonatal brain atlas of healthy subjects that can be applied to multi-modal MRI data. Structural and diffusion 3T MRI scans were acquired soon after birth from 33 typically developing neonates born at term (mean postmenstrual age at birth 39(+5) weeks, range 37(+2)-41(+6)). An adult brain atlas (SRI24/TZO) was propagated to the neonatal data using temporal registration via childhood templates with dense temporal samples (NIH Pediatric Database), with the final atlas (Edinburgh Neonatal Atlas, ENA33) constructed using the Symmetric Group Normalization (SyGN) method. After this step, the computed final transformations were applied to T2-weighted data, and fractional anisotropy, mean diffusivity, and tissue segmentations to provide a multi-modal atlas with 107 anatomical regions; a symmetric version was also created to facilitate studies of laterality. Volumes of each region of interest were measured to provide reference data from normal subjects. Because this atlas is generated from step-wise propagation of adult labels through intermediate time points in childhood, it may serve as a useful starting point for modeling brain growth during development. PMID:27242423

  11. Parcellation of the Healthy Neonatal Brain into 107 Regions Using Atlas Propagation through Intermediate Time Points in Childhood

    PubMed Central

    Blesa, Manuel; Serag, Ahmed; Wilkinson, Alastair G.; Anblagan, Devasuda; Telford, Emma J.; Pataky, Rozalia; Sparrow, Sarah A.; Macnaught, Gillian; Semple, Scott I.; Bastin, Mark E.; Boardman, James P.

    2016-01-01

    Neuroimage analysis pipelines rely on parcellated atlases generated from healthy individuals to provide anatomic context to structural and diffusion MRI data. Atlases constructed using adult data introduce bias into studies of early brain development. We aimed to create a neonatal brain atlas of healthy subjects that can be applied to multi-modal MRI data. Structural and diffusion 3T MRI scans were acquired soon after birth from 33 typically developing neonates born at term (mean postmenstrual age at birth 39+5 weeks, range 37+2–41+6). An adult brain atlas (SRI24/TZO) was propagated to the neonatal data using temporal registration via childhood templates with dense temporal samples (NIH Pediatric Database), with the final atlas (Edinburgh Neonatal Atlas, ENA33) constructed using the Symmetric Group Normalization (SyGN) method. After this step, the computed final transformations were applied to T2-weighted data, and fractional anisotropy, mean diffusivity, and tissue segmentations to provide a multi-modal atlas with 107 anatomical regions; a symmetric version was also created to facilitate studies of laterality. Volumes of each region of interest were measured to provide reference data from normal subjects. Because this atlas is generated from step-wise propagation of adult labels through intermediate time points in childhood, it may serve as a useful starting point for modeling brain growth during development. PMID:27242423

  12. A Probabilistic Atlas of Diffuse WHO Grade II Glioma Locations in the Brain

    PubMed Central

    Baumann, Cédric; Zouaoui, Sonia; Yordanova, Yordanka; Blonski, Marie; Rigau, Valérie; Chemouny, Stéphane; Taillandier, Luc; Bauchet, Luc; Duffau, Hugues; Paragios, Nikos

    2016-01-01

    Diffuse WHO grade II gliomas are diffusively infiltrative brain tumors characterized by an unavoidable anaplastic transformation. Their management is strongly dependent on their location in the brain due to interactions with functional regions and potential differences in molecular biology. In this paper, we present the construction of a probabilistic atlas mapping the preferential locations of diffuse WHO grade II gliomas in the brain. This is carried out through a sparse graph whose nodes correspond to clusters of tumors clustered together based on their spatial proximity. The interest of such an atlas is illustrated via two applications. The first one correlates tumor location with the patient’s age via a statistical analysis, highlighting the interest of the atlas for studying the origins and behavior of the tumors. The second exploits the fact that the tumors have preferential locations for automatic segmentation. Through a coupled decomposed Markov Random Field model, the atlas guides the segmentation process, and characterizes which preferential location the tumor belongs to and consequently which behavior it could be associated to. Leave-one-out cross validation experiments on a large database highlight the robustness of the graph, and yield promising segmentation results. PMID:26751577

  13. A Probabilistic Atlas of Diffuse WHO Grade II Glioma Locations in the Brain.

    PubMed

    Parisot, Sarah; Darlix, Amélie; Baumann, Cédric; Zouaoui, Sonia; Yordanova, Yordanka; Blonski, Marie; Rigau, Valérie; Chemouny, Stéphane; Taillandier, Luc; Bauchet, Luc; Duffau, Hugues; Paragios, Nikos

    2016-01-01

    Diffuse WHO grade II gliomas are diffusively infiltrative brain tumors characterized by an unavoidable anaplastic transformation. Their management is strongly dependent on their location in the brain due to interactions with functional regions and potential differences in molecular biology. In this paper, we present the construction of a probabilistic atlas mapping the preferential locations of diffuse WHO grade II gliomas in the brain. This is carried out through a sparse graph whose nodes correspond to clusters of tumors clustered together based on their spatial proximity. The interest of such an atlas is illustrated via two applications. The first one correlates tumor location with the patient's age via a statistical analysis, highlighting the interest of the atlas for studying the origins and behavior of the tumors. The second exploits the fact that the tumors have preferential locations for automatic segmentation. Through a coupled decomposed Markov Random Field model, the atlas guides the segmentation process, and characterizes which preferential location the tumor belongs to and consequently which behavior it could be associated to. Leave-one-out cross validation experiments on a large database highlight the robustness of the graph, and yield promising segmentation results. PMID:26751577

  14. Visualizing the spatial gene expression organization in the brain through non-linear similarity embeddings.

    PubMed

    Mahfouz, Ahmed; van de Giessen, Martijn; van der Maaten, Laurens; Huisman, Sjoerd; Reinders, Marcel; Hawrylycz, Michael J; Lelieveldt, Boudewijn P F

    2015-02-01

    The Allen Brain Atlases enable the study of spatially resolved, genome-wide gene expression patterns across the mammalian brain. Several explorative studies have applied linear dimensionality reduction methods such as Principal Component Analysis (PCA) and classical Multi-Dimensional Scaling (cMDS) to gain insight into the spatial organization of these expression patterns. In this paper, we describe a non-linear embedding technique called Barnes-Hut Stochastic Neighbor Embedding (BH-SNE) that emphasizes the local similarity structure of high-dimensional data points. By applying BH-SNE to the gene expression data from the Allen Brain Atlases, we demonstrate the consistency of the 2D, non-linear embedding of the sagittal and coronal mouse brain atlases, and across 6 human brains. In addition, we quantitatively show that BH-SNE maps are superior in their separation of neuroanatomical regions in comparison to PCA and cMDS. Finally, we assess the effect of higher-order principal components on the global structure of the BH-SNE similarity maps. Based on our observations, we conclude that BH-SNE maps with or without prior dimensionality reduction (based on PCA) provide comprehensive and intuitive insights in both the local and global spatial transcriptome structure of the human and mouse Allen Brain Atlases. PMID:25449901

  15. Semi-Automated Atlas-based Analysis of Brain Histological Sections

    PubMed Central

    Kopec, Charles D.; Bowers, Amanda C.; Pai, Shraddha; Brody, Carlos D.

    2011-01-01

    Quantifying the location and/or number of features in a histological section of the brain currently requires one to first, manually register a corresponding section from a tissue atlas onto the experimental section and second, count the features. No automated method exists for the first process (registering), and most automated methods for the second process (feature counting) operate reliably only in a high signal-to-noise regime. To reduce experimenter bias and inconsistencies and increase the speed of these analyses, we developed Atlas Fitter, a semi-automated, open-source MatLab-based software package that assists in rapidly registering atlas panels onto histological sections. We also developed CellCounter, a novel fully-automated cell counting algorithm that is designed to operate on images with non-uniform background intensities and low signal-to-noise ratios. PMID:21194546

  16. Implementation of talairach atlas based automated brain segmentation for radiation therapy dosimetry.

    PubMed

    Popple, R A; Griffith, H R; Sawrie, S M; Fiveash, J B; Brezovich, I A

    2006-02-01

    Radiotherapy for brain cancer inevitably results in irradiation of uninvolved brain. While it has been demonstrated that irradiation of the brain can result in cognitive deficits, dose-volume relationships are not well established. There is little work correlating a particular cognitive deficit with dose received by the region of the brain responsible for the specific cognitive function. One obstacle to such studies is that identification of brain anatomy is both labor intensive and dependent on the individual performing the segmentation. Automatic segmentation has the potential to be both efficient and consistent. Brains2 is a software package developed by the University of Iowa for MRI volumetric studies. It utilizes MR images, the Talairach atlas, and an artificial neural network (ANN) to segment brain images into substructures in a standardized manner. We have developed a software package, Brains2DICOM, that converts the regions of interest identified by Brains2 into a DICOM radiotherapy structure set. The structure set can be imported into a treatment planning system for dosimetry. We demonstrated the utility of Brains2DICOM using a test case, a 34-year-old man with diffuse astrocytoma treated with three-dimensional conformal radiotherapy. Brains2 successfully applied the Talairach atlas to identify the right and left frontal, parietal, temporal, occipital, subcortical, and cerebellum regions. Brains2 was not successful in applying the ANN to identify small structures, such as the hippocampus and caudate. Further work is necessary to revise the ANN or to develop new methods for identification of small structures in the presence of disease and radiation induced changes. The segmented regions-of-interest were transferred to our commercial treatment planning system using DICOM and dose-volume histograms were constructed. This method will facilitate the acquisition of data necessary for the development of normal tissue complication probability (NTCP) models that

  17. Construction of a neuroanatomical shape complex atlas from 3D MRI brain structures.

    PubMed

    Chen, Ting; Rangarajan, Anand; Eisenschenk, Stephan J; Vemuri, Baba C

    2012-04-15

    Brain atlas construction has attracted significant attention lately in the neuroimaging community due to its application to the characterization of neuroanatomical shape abnormalities associated with various neurodegenerative diseases or neuropsychiatric disorders. Existing shape atlas construction techniques usually focus on the analysis of a single anatomical structure in which the important inter-structural information is lost. This paper proposes a novel technique for constructing a neuroanatomical shape complex atlas based on an information geometry framework. A shape complex is a collection of neighboring shapes - for example, the thalamus, amygdala and the hippocampus circuit - which may exhibit changes in shape across multiple structures during the progression of a disease. In this paper, we represent the boundaries of the entire shape complex using the zero level set of a distance transform function S(x). We then re-derive the relationship between the stationary state wave function ψ(x) of the Schrödinger equation [formula in text] and the eikonal equation [formula in text] satisfied by any distance function. This leads to a one-to-one map (up to scale) between ψ(x) and S(x) via an explicit relationship. We further exploit this relationship by mapping ψ(x) to a unit hypersphere whose Riemannian structure is fully known, thus effectively turn ψ(x) into the square-root of a probability density function. This allows us to make comparisons - using elegant, closed-form analytic expressions - between shape complexes represented as square-root densities. A shape complex atlas is constructed by computing the Karcher mean ψ¯(x) in the space of square-root densities and then inversely mapping it back to the space of distance transforms in order to realize the atlas shape. We demonstrate the shape complex atlas computation technique via a set of experiments on a population of brain MRI scans including controls and epilepsy patients with either right anterior

  18. Construction of a Deformable Spatiotemporal MRI Atlas of the Fetal Brain: Evaluation of Similarity Metrics and Deformation Models

    PubMed Central

    Gholipour, Ali; Limperopoulos, Catherine; Clancy, Sean; Clouchoux, Cedric; Akhondi-Asl, Alireza; Estroff, Judy A.; Warfield, Simon K.

    2014-01-01

    The development and identification of best methods in fetal brain MRI analysis is crucial as we expect an outburst of studies on groupwise and longitudinal analysis of early brain development in the upcoming years. To address this critical need, in this paper, we have developed a mathematical framework for the construction of an unbiased deformable spatiotemporal atlas of the fetal brain MRI and compared it to alternative configurations in terms of similarity metrics and deformation models. Our contributions are twofold: first we suggest a novel approach to fetal brain spatiotemporal atlas construction that shows high capability in capturing anatomic variation between subjects; and second, within our atlas construction framework we evaluate and compare a set of plausible configurations for inter-subject fetal brain MRI registration and identify the most accurate approach that can potentially lead to most accurate results in population atlas construction, atlas-based segmentation, and group analysis. Our evaluation results indicate that symmetric diffeomorphic deformable registration with cross correlation similarity metric outperforms other configurations in this application and results in sharp unbiased atlases that can be used in fetal brain MRI analysis. PMID:25485391

  19. Workflow and atlas system for brain-wide mapping of axonal connectivity in rat.

    PubMed

    Zakiewicz, Izabela M; van Dongen, Yvette C; Leergaard, Trygve B; Bjaalie, Jan G

    2011-01-01

    Detailed knowledge about the anatomical organization of axonal connections is important for understanding normal functions of brain systems and disease-related dysfunctions. Such connectivity data are typically generated in neuroanatomical tract-tracing experiments in which specific axonal connections are visualized in histological sections. Since journal publications typically only accommodate restricted data descriptions and example images, literature search is a cumbersome way to retrieve overviews of brain connectivity. To explore more efficient ways of mapping, analyzing, and sharing detailed axonal connectivity data from the rodent brain, we have implemented a workflow for data production and developed an atlas system tailored for online presentation of axonal tracing data. The system is available online through the Rodent Brain WorkBench (www.rbwb.org; Whole Brain Connectivity Atlas) and holds experimental metadata and high-resolution images of histological sections from experiments in which axonal tracers were injected in the primary somatosensory cortex. We here present the workflow and the data system, and exemplify how the online image repository can be used to map different aspects of the brain-wide connectivity of the rat primary somatosensory cortex, including not only presence of connections but also morphology, densities, and spatial organization. The accuracy of the approach is validated by comparing results generated with our system with findings reported in previous publications. The present study is a contribution to a systematic mapping of rodent brain connections and represents a starting point for further large-scale mapping efforts. PMID:21829640

  20. The brain of the common vampire bat, Desmodus rotundus murinus (Wagner, 1840): a cytoarchitectural atlas.

    PubMed

    Bhatnagar, K P

    2008-08-01

    The vampire bat, Desmodus rotundus, is exceptionally agile and stealthy in nature. Feeding at night on cattle blood, it is a known scourge carrying rabies. It is endowed with a very high neocortical volume among bats, acute olfactory capabilities and an accessory olfactory system. These characteristics have resulted into an impressive number of neuroanatomical investigations except a long due atlas on its brain. This study presents a cytoarchitectural atlas of the brain of the common vampire, Desmodus rotundus murinus, in the frontal plane, serially between the olfactory bulb and the medulla oblongata. Twenty six selected sections are presented, each separated by about 300 to 560 microns. The atlas figures show lugol fast blue-cresyl echt violet stained hemisections with their matching half in a labeled line drawing. About 595 discrete brain structures (some repeating) have been identified. This study is likely to provide the accurate localization of nuclear groups, whole structures, fiber tracts, and interconnections to facilitate future neuroanatomical and neurophysiological investigations on the vampire brain. PMID:18833481

  1. A Multi-Atlas Based Method for Automated Anatomical Rat Brain MRI Segmentation and Extraction of PET Activity

    PubMed Central

    Lancelot, Sophie; Roche, Roxane; Slimen, Afifa; Bouillot, Caroline; Levigoureux, Elise; Langlois, Jean-Baptiste; Zimmer, Luc; Costes, Nicolas

    2014-01-01

    Introduction Preclinical in vivo imaging requires precise and reproducible delineation of brain structures. Manual segmentation is time consuming and operator dependent. Automated segmentation as usually performed via single atlas registration fails to account for anatomo-physiological variability. We present, evaluate, and make available a multi-atlas approach for automatically segmenting rat brain MRI and extracting PET activies. Methods High-resolution 7T 2DT2 MR images of 12 Sprague-Dawley rat brains were manually segmented into 27-VOI label volumes using detailed protocols. Automated methods were developed with 7/12 atlas datasets, i.e. the MRIs and their associated label volumes. MRIs were registered to a common space, where an MRI template and a maximum probability atlas were created. Three automated methods were tested: 1/registering individual MRIs to the template, and using a single atlas (SA), 2/using the maximum probability atlas (MP), and 3/registering the MRIs from the multi-atlas dataset to an individual MRI, propagating the label volumes and fusing them in individual MRI space (propagation & fusion, PF). Evaluation was performed on the five remaining rats which additionally underwent [18F]FDG PET. Automated and manual segmentations were compared for morphometric performance (assessed by comparing volume bias and Dice overlap index) and functional performance (evaluated by comparing extracted PET measures). Results Only the SA method showed volume bias. Dice indices were significantly different between methods (PF>MP>SA). PET regional measures were more accurate with multi-atlas methods than with SA method. Conclusions Multi-atlas methods outperform SA for automated anatomical brain segmentation and PET measure’s extraction. They perform comparably to manual segmentation for FDG-PET quantification. Multi-atlas methods are suitable for rapid reproducible VOI analyses. PMID:25330005

  2. New experimental results in atlas-based brain morphometry

    NASA Astrophysics Data System (ADS)

    Gee, James C.; Fabella, Brian A.; Fernandes, Siddharth E.; Turetsky, Bruce I.; Gur, Ruben C.; Gur, Raquel E.

    1999-05-01

    In a previous meeting, we described a computational approach to MRI morphometry, in which a spatial warp mapping a reference or atlas image into anatomic alignment with the subject is first inferred. Shape differences with respect to the atlas are then studied by calculating the pointwise Jacobian determinant for the warp, which provides a measure of the change in differential volume about a point in the reference as it transforms to its corresponding position in the subject. In this paper, the method is used to analyze sex differences in the shape and size of the corpus callosum in an ongoing study of a large population of normal controls. The preliminary results of the current analysis support findings in the literature that have observed the splenium to be larger in females than in males.

  3. A Bayesian approach to the creation of a study-customized neonatal brain atlas

    PubMed Central

    Zhang, Yajing; Chang, Linda; Ceritoglu, Can; Skranes, Jon; Ernst, Thomas; Mori, Susumu; Miller, Michael I.; Oishi, Kenichi

    2014-01-01

    Atlas-based image analysis (ABA), in which an anatomical “parcellation map” is used for parcel-by-parcel image quantification, is widely used to analyze anatomical and functional changes related to brain development, aging, and various diseases. The parcellation maps are often created based on common MRI templates, which allow users to transform the template to target images, or vice versa, to perform parcel-by-parcel statistics, and report the scientific findings based on common anatomical parcels. The use of a study-specific template, which represents the anatomical features of the study population better than common templates, is preferable for accurate anatomical labeling; however, the creation of a parcellation map for a study-specific template is extremely labor intensive, and the definitions of anatomical boundaries are not necessarily compatible with those of the common template. In this study, we employed a Volume-based Template Estimation (VTE) method to create a neonatal brain template customized to a study population, while keeping the anatomical parcellation identical to that of a common MRI atlas. The VTE was used to morph the standardized parcellation map of the JHU-neonate-SS atlas to capture the anatomical features of a study population. The resultant “study-customized” T1-weighted and diffusion tensor imaging (DTI) template, with three-dimensional anatomical parcellation that defined 122 brain regions, was compared with the JHU-neonate-SS atlas, in terms of the registration accuracy. A pronounced increase in the accuracy of cortical parcellation and superior tensor alignment were observed when the customized template was used. With the customized atlas-based analysis, the fractional anisotropy (FA) detected closely approximated the manual measurements. This tool provides a solution for achieving normalization-based measurements with increased accuracy, while reporting scientific findings in a consistent framework. PMID:25026155

  4. Non-local Atlas-guided Multi-channel Forest Learning for Human Brain Labeling

    PubMed Central

    Ma, Guangkai; Gao, Yaozong; Wu, Guorong; Wu, Ligang; Shen, Dinggang

    2015-01-01

    Labeling MR brain images into anatomically meaningful regions is important in many quantitative brain researches. In many existing label fusion methods, appearance information is widely used. Meanwhile, recent progress in computer vision suggests that the context feature is very useful in identifying an object from a complex scene. In light of this, we propose a novel learning-based label fusion method by using both low-level appearance features (computed from the target image) and high-level context features (computed from warped atlases or tentative labeling maps of the target image). In particular, we employ a multi-channel random forest to learn the nonlinear relationship between these hybrid features and the target labels (i.e., corresponding to certain anatomical structures). Moreover, to accommodate the high inter-subject variations, we further extend our learning-based label fusion to a multi-atlas scenario, i.e., we train a random forest for each atlas and then obtain the final labeling result according to the consensus of all atlases. We have comprehensively evaluated our method on both LONI-LBPA40 and IXI datasets, and achieved the highest labeling accuracy, compared to the state-of-the-art methods in the literature. PMID:26942235

  5. Development of representative magnetic resonance imaging-based atlases of the canine brain and evaluation of three methods for atlas-based segmentation.

    PubMed

    Milne, Marjorie E; Steward, Christopher; Firestone, Simon M; Long, Sam N; O'Brien, Terrence J; Moffat, Bradford A

    2016-04-01

    OBJECTIVE To develop representative MRI atlases of the canine brain and to evaluate 3 methods of atlas-based segmentation (ABS). ANIMALS 62 dogs without clinical signs of epilepsy and without MRI evidence of structural brain disease. PROCEDURES The MRI scans from 44 dogs were used to develop 4 templates on the basis of brain shape (brachycephalic, mesaticephalic, dolichocephalic, and combined mesaticephalic and dolichocephalic). Atlas labels were generated by segmenting the brain, ventricular system, hippocampal formation, and caudate nuclei. The MRI scans from the remaining 18 dogs were used to evaluate 3 methods of ABS (manual brain extraction and application of a brain shape-specific template [A], automatic brain extraction and application of a brain shape-specific template [B], and manual brain extraction and application of a combined template [C]). The performance of each ABS method was compared by calculation of the Dice and Jaccard coefficients, with manual segmentation used as the gold standard. RESULTS Method A had the highest mean Jaccard coefficient and was the most accurate ABS method assessed. Measures of overlap for ABS methods that used manual brain extraction (A and C) ranged from 0.75 to 0.95 and compared favorably with repeated measures of overlap for manual extraction, which ranged from 0.88 to 0.97. CONCLUSIONS AND CLINICAL RELEVANCE Atlas-based segmentation was an accurate and repeatable method for segmentation of canine brain structures. It could be performed more rapidly than manual segmentation, which should allow the application of computer-assisted volumetry to large data sets and clinical cases and facilitate neuroimaging research and disease diagnosis. PMID:27027839

  6. Multi-Contrast Human Neonatal Brain Atlas: Application to Normal Neonate Development Analysis

    PubMed Central

    Oishi, Kenichi; Mori, Susumu; Donohue, Pamela K.; Ernst, Thomas; Anderson, Lynn; Buchthal, Steven; Faria, Andreia; Jiang, Hangyi; Li, Xin; Miller, Michael I.; van Zijl, Peter C.M.; Chang, Linda

    2011-01-01

    MRI is a sensitive method for detecting subtle anatomic abnormalities in the neonatal brain. To optimize the usefulness for neonatal and pediatric care, systematic research, based on quantitative image analysis and functional correlation, is required. Normalization-based image analysis is one of the most effective methods for image quantification and statistical comparison. However, the application of this methodology to neonatal brain MRI scans is rare. Some of the difficulties are the rapid changes in T1 and T2 contrasts and the lack of contrast between brain structures, which prohibits accurate cross-subject image registration. Diffusion tensor imaging (DTI), which provides rich and quantitative anatomical contrast in neonate brains, is an ideal technology for normalization–based neonatal brain analysis. In this paper, we report the development of neonatal brain atlases with detailed anatomic information derived from DTI and co-registered anatomical MRI. Combined with a diffeomorphic transformation, we were able to normalize neonatal brain images to the atlas space and three-dimensionally parcellate images into 122 regions. The accuracy of the normalization was comparable to the reliability of human raters. This method was then applied to babies of 37 to 53 post-conceptional weeks to characterize developmental changes of the white matter, which indicated a posterior-to-anterior and a central-to-peripheral direction of maturation. We expect that future applications of this atlas will include investigations of the effect of prenatal events and the effects of preterm birth or low birth weights, as well as clinical applications, such as determining imaging biomarkers for various neurological disorders. PMID:21276861

  7. A 3-dimensional digital atlas of the ascending sensory and the descending motor systems in the pigeon brain.

    PubMed

    Güntürkün, Onur; Verhoye, Marleen; De Groof, Geert; Van der Linden, Annemie

    2013-01-01

    Pigeons are classic animal models for learning, memory, and cognition. The majority of the current understanding about avian neurobiology outside of the domain of the song system has been established using pigeons. Since MRI represents an increasingly relevant tool for comparative neuroscience, a 3-dimensional MRI-based atlas of the pigeon brain becomes essential. Using multiple imaging protocols, we delineated diverse ascending sensory and descending motor systems as well as the hippocampal formation. This pigeon brain atlas can easily be used to determine the stereotactic location of identified neural structures at any angle of the head. In addition, the atlas is useful to find the optimal angle of sectioning for slice experiments, stereotactic injections and electrophysiological recordings. This pigeon brain atlas is freely available for the scientific community. PMID:22367250

  8. A three-dimensional stereotaxic MRI brain atlas of the cichlid fish Oreochromis mossambicus.

    PubMed

    Simões, José M; Teles, Magda C; Oliveira, Rui F; Van der Linden, Annemie; Verhoye, Marleen

    2012-01-01

    The African cichlid Oreochromis mossambicus (Mozambique tilapia) has been used as a model system in a wide range of behavioural and neurobiological studies. The increasing number of genetic tools available for this species, together with the emerging interest in its use for neurobiological studies, increased the need for an accurate hodological mapping of the tilapia brain to supplement the available histological data. The goal of our study was to elaborate a three-dimensional, high-resolution digital atlas using magnetic resonance imaging, supported by Nissl staining. Resulting images were viewed and analysed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. This high resolution tilapia brain atlas is expected to become a very useful tool for neuroscientists using this fish model and will certainly expand their use in future studies regarding the central nervous system. PMID:22984463

  9. Atlas-based fuzzy connectedness segmentation and intensity nonuniformity correction applied to brain MRI.

    PubMed

    Zhou, Yongxin; Bai, Jing

    2007-01-01

    A framework that combines atlas registration, fuzzy connectedness (FC) segmentation, and parametric bias field correction (PABIC) is proposed for the automatic segmentation of brain magnetic resonance imaging (MRI). First, the atlas is registered onto the MRI to initialize the following FC segmentation. Original techniques are proposed to estimate necessary initial parameters of FC segmentation. Further, the result of the FC segmentation is utilized to initialize a following PABIC algorithm. Finally, we re-apply the FC technique on the PABIC corrected MRI to get the final segmentation. Thus, we avoid expert human intervention and provide a fully automatic method for brain MRI segmentation. Experiments on both simulated and real MRI images demonstrate the validity of the method, as well as the limitation of the method. Being a fully automatic method, it is expected to find wide applications, such as three-dimensional visualization, radiation therapy planning, and medical database construction. PMID:17260863

  10. A brain MRI atlas of the common squirrel monkey, Saimiri sciureus

    NASA Astrophysics Data System (ADS)

    Gao, Yurui; Schilling, Kurt G.; Khare, Shweta P.; Panda, Swetasudha; Choe, Ann S.; Stepniewska, Iwona; Li, Xia; Ding, Zhoahua; Anderson, Adam; Landman, Bennett A.

    2014-03-01

    The common squirrel monkey, Saimiri sciureus, is a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. It is one of the most commonly used South American primates in biomedical research. Unlike its Old World macaque cousins, no digital atlases have described the organization of the squirrel monkey brain. Here, we present a multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. In vivo MRI acquisitions include high resolution T2 structural imaging and low resolution diffusion tensor imaging. Ex vivo MRI acquisitions include high resolution T2 structural imaging and high resolution diffusion tensor imaging. Cortical regions were manually annotated on the co-registered volumes based on published histological sections.

  11. H. Julian Allen

    NASA Technical Reports Server (NTRS)

    1957-01-01

    H. Julian Allen stands beside the observation window of the 8 x 7 foot test section of the NACA Ames Unitary Plan Wind Tunnel. H. Julian Allen is best known for his 'Blunt Body Theory' of aerodynamics, a design technique for alleviating the severe re-entry heating problem which was then delaying the development of ballistic missiles. His findings revolutionized the fundamental design of ballistic missle re-entry shapes. Subsequently, applied research led to applications of the 'blunt' shape to ballistic missles and spacecraft which were intended to re-enter the Earth's atmosphere. This application led to the design of ablative heat shields that protected the Mercury, Gemini and Apollo astronauts as their space capsules re- entered the Earth's atmosphere. 'Harvey' Allen as he was called by most, was not only a brilliant scientist and aeronautical engineer but was also admired for his kindness, thoughtfulness and sense of humor. Among his many other accomplishments, Harvey Allen served as Center Director of the NASA Ames Research Center from 1965 to 1969. He died of a heart attack on January 29, 1977 at the age of 66.

  12. Screw-Retaining Allen Wrench

    NASA Technical Reports Server (NTRS)

    Granett, D.

    1985-01-01

    Steadying screws with fingers unnecessary. Crimp in uncompressed spring wire slightly protrudes from one facet of Allen wrench. Compressed spring retains Allen screw. Tool used with Allen-head screws in cramped spaces with little or no room for fingers to hold fastener while turned by wrench.

  13. Evaluation of Cross-Protocol Stability of a Fully Automated Brain Multi-Atlas Parcellation Tool

    PubMed Central

    Liang, Zifei; He, Xiaohai; Ceritoglu, Can; Tang, Xiaoying; Li, Yue; Kutten, Kwame S.; Oishi, Kenichi; Miller, Michael I.; Mori, Susumu; Faria, Andreia V.

    2015-01-01

    Brain parcellation tools based on multiple-atlas algorithms have recently emerged as a promising method with which to accurately define brain structures. When dealing with data from various sources, it is crucial that these tools are robust for many different imaging protocols. In this study, we tested the robustness of a multiple-atlas, likelihood fusion algorithm using Alzheimer’s Disease Neuroimaging Initiative (ADNI) data with six different protocols, comprising three manufacturers and two magnetic field strengths. The entire brain was parceled into five different levels of granularity. In each level, which defines a set of brain structures, ranging from eight to 286 regions, we evaluated the variability of brain volumes related to the protocol, age, and diagnosis (healthy or Alzheimer’s disease). Our results indicated that, with proper pre-processing steps, the impact of different protocols is minor compared to biological effects, such as age and pathology. A precise knowledge of the sources of data variation enables sufficient statistical power and ensures the reliability of an anatomical analysis when using this automated brain parcellation tool on datasets from various imaging protocols, such as clinical databases. PMID:26208327

  14. Implementation of nonlinear registration of brain atlas based on piecewise grid system

    NASA Astrophysics Data System (ADS)

    Liu, Rong; Gu, Lixu; Xu, Jianrong

    2007-12-01

    In this paper, a multi-step registration method of brain atlas and clinical Magnetic Resonance Imaging (MRI) data based on Thin-Plate Splines (TPS) and Piecewise Grid System (PGS) is presented. The method can help doctors to determine the corresponding anatomical structure between patient image and the brain atlas by piecewise nonlinear registration. Since doctors mostly pay attention to particular Region of Interest (ROI), and a global nonlinear registration is quite time-consuming which is not suitable for real-time clinical application, we propose a novel method to conduct linear registration in global area before nonlinear registration is performed in selected ROI. The homogenous feature points are defined to calculate the transform matrix between patient data and the brain atlas to conclude the mapping function. Finally, we integrate the proposed approach into an application of neurosurgical planning and guidance system which lends great efficiency in both neuro-anatomical education and guiding of neurosurgical operations. The experimental results reveal that the proposed approach can keep an average registration error of 0.25mm in near real-time manner.

  15. A hybrid hierarchical approach for brain tissue segmentation by combining brain atlas and least square support vector machine.

    PubMed

    Kasiri, Keyvan; Kazemi, Kamran; Dehghani, Mohammad Javad; Helfroush, Mohammad Sadegh

    2013-10-01

    In this paper, we present a new semi-automatic brain tissue segmentation method based on a hybrid hierarchical approach that combines a brain atlas as a priori information and a least-square support vector machine (LS-SVM). The method consists of three steps. In the first two steps, the skull is removed and the cerebrospinal fluid (CSF) is extracted. These two steps are performed using the toolbox FMRIB's automated segmentation tool integrated in the FSL software (FSL-FAST) developed in Oxford Centre for functional MRI of the brain (FMRIB). Then, in the third step, the LS-SVM is used to segment grey matter (GM) and white matter (WM). The training samples for LS-SVM are selected from the registered brain atlas. The voxel intensities and spatial positions are selected as the two feature groups for training and test. SVM as a powerful discriminator is able to handle nonlinear classification problems; however, it cannot provide posterior probability. Thus, we use a sigmoid function to map the SVM output into probabilities. The proposed method is used to segment CSF, GM and WM from the simulated magnetic resonance imaging (MRI) using Brainweb MRI simulator and real data provided by Internet Brain Segmentation Repository. The semi-automatically segmented brain tissues were evaluated by comparing to the corresponding ground truth. The Dice and Jaccard similarity coefficients, sensitivity and specificity were calculated for the quantitative validation of the results. The quantitative results show that the proposed method segments brain tissues accurately with respect to corresponding ground truth. PMID:24696800

  16. Atlas of positron emission tomography of the brain

    SciTech Connect

    Heiss, W.; Beil, C.; Herholz, K.; Pavlik, G.; Wagner, R.; Weinhard, K.

    1985-01-01

    The aim and scope of this atlas are expressed in its title. The text and legends of the book are presented in both German and English. The book contains 12 high-quality color illustrations culled from nine tomography centers across Europe and North America. Almost two-thirds of the book is devoted to the measurement of regional cerebral glucose metabolism and cerebral blood flow. The remainder manages to cover all of the other cerebral applications of positron emission tomography (PET). The authors discuss that PET is being used principally in research and that its future, although theoretically unlimited, depends on the development of ''further labeled compounds.''

  17. Automatic atlas-based volume estimation of human brain regions from MR images

    SciTech Connect

    Andreasen, N.C.; Rajarethinam, R.; Cizadlo, T.; Arndt, S.

    1996-01-01

    MRI offers many opportunities for noninvasive in vivo measurement of structure-function relationships in the human brain. Although automated methods are now available for whole-brain measurements, an efficient and valid automatic method for volume estimation of subregions such as the frontal or temporal lobes is still needed. We adapted the Talairach atlas to the study of brain subregions. We supplemented the atlas with additional boxes to include the cerebellum. We assigned all the boxes to 1 of 12 regions of interest (ROIs) (frontal, parietal, temporal, and occipital lobes, cerebellum, and subcortical regions on right and left sides of the brain).Using T1-weighted MR scans collected with an SPGR sequence (slice thickness = 1.5 mm), we manually traced these ROIs and produced volume estimates. We then transformed the scans into Talairach space and compared the volumes produced by the two methods ({open_quotes}traced{close_quotes} versus {open_quotes}automatic{close_quotes}). The traced measurements were considered to be the {open_quotes}gold standard{close_quotes} against which the automatic measurements were compared. The automatic method was found to produce measurements that were nearly identical to the traced method. We compared absolute measurements of volume produced by the two methods, as well as the sensitivity and specificity of the automatic method. We also compared the measurements of cerebral blood flow obtained through [{sup 15}O]H{sub 2}O PET studies in a sample of nine subjects. Absolute measurements of volume produced by the two methods were very similar, and the sensitivity and specificity of the automatic method were found to be high for all regions. The flow values were also found to be very similar by both methods. The automatic atlas-based method for measuring the volume of brain subregions produces results that are similar to manual techniques. 39 refs., 4 figs., 3 tabs.

  18. A rat brain MRI template with digital stereotaxic atlas of fine anatomical delineations in paxinos space and its automated application in voxel-wise analysis.

    PubMed

    Nie, Binbin; Chen, Kewei; Zhao, Shujun; Liu, Junhua; Gu, Xiaochun; Yao, Qunli; Hui, Jiaojie; Zhang, Zhijun; Teng, Gaojun; Zhao, Chunjie; Shan, Baoci

    2013-06-01

    This study constructs a rat brain T2 -weighted magnetic resonance imaging template including olfactory bulb and a compatible digital atlas. The atlas contains 624 carefully delineated brain structures based on the newest (2005) edition of rat brain atlas by Paxinos and Watson. An automated procedure, as an SPM toolbox, was introduced for spatially normalizing individual rat brains, conducting statistical analysis and visually localizing the results in the Atlas coordinate space. The brain template/atlas and the procedure were evaluated using functional images between rats with the right side middle cerebral artery occlusion (MCAO) and normal controls. The result shows that the brain region with significant signal decline in the MCAO rats was consistent with the occlusion position. PMID:22287270

  19. EPICS: Allen-Bradley hardware reference manual

    SciTech Connect

    Nawrocki, G.

    1993-04-05

    This manual covers the following hardware: Allen-Bradley 6008 -- SV VMEbus I/O scanner; Allen-Bradley universal I/O chassis 1771-A1B, -A2B, -A3B, and -A4B; Allen-Bradley power supply module 1771-P4S; Allen-Bradley 1771-ASB remote I/O adapter module; Allen-Bradley 1771-IFE analog input module; Allen-Bradley 1771-OFE analog output module; Allen-Bradley 1771-IG(D) TTL input module; Allen-Bradley 1771-OG(d) TTL output; Allen-Bradley 1771-IQ DC selectable input module; Allen-Bradley 1771-OW contact output module; Allen-Bradley 1771-IBD DC (10--30V) input module; Allen-Bradley 1771-OBD DC (10--60V) output module; Allen-Bradley 1771-IXE thermocouple/millivolt input module; and the Allen-Bradley 2705 RediPANEL push button module.

  20. Three-dimensional reconstruction of brain structures of the rodent Octodon degus: a brain atlas constructed by combining histological and magnetic resonance images.

    PubMed

    Kumazawa-Manita, Noriko; Katayama, Mariko; Hashikawa, Tsutomu; Iriki, Atsushi

    2013-11-01

    Degus (Octodon degus) are rodents that are becoming more widely used in the neuroscience field. Degus display several more complex behaviors than rats and mice, including complicated social behaviors, vocal communications, and tool usage with superb manual dexterity. However, relatively little information is known about the anatomy of degu brains. Therefore, for these complex behaviors to be correlated with specific brain regions, a contemporary atlas of the degu brain is required. This manuscript describes the construction of a three-dimensional (3D) volume rendered model of the degu brain that combines histological and magnetic resonance images. This atlas provides several advantages, including the ability to visualize the surface of the brain from any angle. The atlas also permits virtual cutting of brain sections in any plane and provides stereotaxic coordinates for all sections, to be beneficial for both experimental surgeries and radiological studies. The reconstructed 3D atlas is freely available online at: http://brainatlas.brain.riken.jp/degu/modules/xoonips/listitem.php?index_id=24 . PMID:23995563

  1. Multi-Object Model-based Multi-Atlas Segmentation for Rodent Brains using Dense Discrete Correspondences

    PubMed Central

    Lee, Joohwi; Kim, Sun Hyung; Styner, Martin

    2016-01-01

    The delineation of rodent brain structures is challenging due to low-contrast multiple cortical and subcortical organs that are closely interfacing to each other. Atlas-based segmentation has been widely employed due to its ability to delineate multiple organs at the same time via image registration. The use of multiple atlases and subsequent label fusion techniques has further improved the robustness and accuracy of atlas-based segmentation. However, the accuracy of atlas-based segmentation is still prone to registration errors; for example, the segmentation of in vivo MR images can be less accurate and robust against image artifacts than the segmentation of post mortem images. In order to improve the accuracy and robustness of atlas-based segmentation, we propose a multi-object, model-based, multi-atlas segmentation method. We first establish spatial correspondences across atlases using a set of dense pseudo-landmark particles. We build a multi-object point distribution model using those particles in order to capture inter- and intra-subject variation among brain structures. The segmentation is obtained by fitting the model into a subject image, followed by label fusion process. Our result shows that the proposed method resulted in greater accuracy than comparable segmentation methods, including a widely used ANTs registration tool. PMID:27065200

  2. Multi-object model-based multi-atlas segmentation for rodent brains using dense discrete correspondences

    NASA Astrophysics Data System (ADS)

    Lee, Joohwi; Kim, Sun Hyung; Styner, Martin

    2016-03-01

    The delineation of rodent brain structures is challenging due to low-contrast multiple cortical and subcortical organs that are closely interfacing to each other. Atlas-based segmentation has been widely employed due to its ability to delineate multiple organs at the same time via image registration. The use of multiple atlases and subsequent label fusion techniques has further improved the robustness and accuracy of atlas-based segmentation. However, the accuracy of atlas-based segmentation is still prone to registration errors; for example, the segmentation of in vivo MR images can be less accurate and robust against image artifacts than the segmentation of post mortem images. In order to improve the accuracy and robustness of atlas-based segmentation, we propose a multi-object, model-based, multi-atlas segmentation method. We first establish spatial correspondences across atlases using a set of dense pseudo-landmark particles. We build a multi-object point distribution model using those particles in order to capture inter- and intra- subject variation among brain structures. The segmentation is obtained by fitting the model into a subject image, followed by label fusion process. Our result shows that the proposed method resulted in greater accuracy than comparable segmentation methods, including a widely used ANTs registration tool.

  3. Multidimensional MRI-CT atlas of the naked mole-rat brain (Heterocephalus glaber).

    PubMed

    Seki, Fumiko; Hikishima, Keigo; Nambu, Sanae; Okanoya, Kazuo; Okano, Hirotaka J; Sasaki, Erika; Miura, Kyoko; Okano, Hideyuki

    2013-01-01

    Naked mole-rats have a variety of distinctive features such as the organization of a hierarchical society (known as eusociality), extraordinary longevity, and cancer resistance; thus, it would be worthwhile investigating these animals in detail. One important task is the preparation of a brain atlas database that provide comprehensive information containing multidimensional data with various image contrasts, which can be achievable using a magnetic resonance imaging (MRI). Advanced MRI techniques such as diffusion tensor imaging (DTI), which generates high contrast images of fiber structures, can characterize unique morphological properties in addition to conventional MRI. To obtain high spatial resolution images, MR histology, DTI, and X-ray computed tomography were performed on the fixed adult brain. Skull and brain structures were segmented as well as reconstructed in stereotaxic coordinates. Data were also acquired for the neonatal brain to allow developmental changes to be observed. Moreover, in vivo imaging of naked mole-rats was established as an evaluation tool of live animals. The data obtained comprised three-dimensional (3D) images with high tissue contrast as well as stereotaxic coordinates. Developmental differences in the visual system were highlighted in particular by DTI. Although it was difficult to delineate optic nerves in the mature adult brain, parts of them could be distinguished in the immature neonatal brain. From observation of cortical thickness, possibility of high somatosensory system development replaced to the visual system was indicated. 3D visualization of brain structures in the atlas as well as the establishment of in vivo imaging would promote neuroimaging researches towards detection of novel characteristics of eusocial naked mole-rats. PMID:24391551

  4. Human Brain White Matter Atlas: Identification and Assignment of Common Anatomical Structures in Superficial White Matter

    PubMed Central

    Oishi, Kenichi; Zilles, Karl; Amunts, Katrin; Faria, Andreia; Jiang, Hangyi; Li, Xin; Akhter, Kazi; Hua, Kegang; Woods, Roger; Toga, Arthur W.; Pike, G. Bruce; Rosa-Neto, Pedro; Evans, Alan; Zhang, Jiangyang; Huang, Hao; Miller, Michael I.; van Zijl, Peter C.M.; Mazziotta, John; Mori, Susumu

    2008-01-01

    Structural delineation and assignment are the fundamental steps in understanding the anatomy of the human brain. The white matter has been structurally defined in the past only at its core regions (deep white matter). However, the most peripheral white matter areas, which are interleaved between the cortex and the deep white matter, have lacked clear anatomical definitions and parcellations. We used axonal fiber alignment information from diffusion tensor imaging (DTI) to delineate the peripheral white matter, and investigated its relationship with the cortex and the deep white matter. Using DTI data from 81 healthy subjects, we identified nine common, blade-like anatomical regions, which were further parcellated into 21 subregions based on the cortical anatomy. Four short association fiber tracts connecting adjacent gyri (U-fibers) were also identified reproducibly among the healthy population. We anticipate that this atlas will be useful resource for atlas-based white matter anatomical studies. PMID:18692144

  5. Construction of Neuroanatomical Shape Complex Atlas from 3D Brain MRI

    PubMed Central

    Chen, Ting; Rangarajan, Anand; Eisenschenk, Stephan J.; Vemuri, Baba C.

    2010-01-01

    This paper proposes a novel technique for constructing a neuroanatomical shape complex atlas using an information geometry framework. A shape complex is a collection of shapes in a local neighborhood. We represent the boundary of the entire shape complex using the zero level set of a distance function S(x). The spatial relations between the different anatomical structures constituting the shape complex are captured via the distance transform. We then leverage the well known relationship between the stationary state wave function ψ(x) of the Schrödinger equation −ħ2∇2ψ + ψ = 0 and the eikonal equation ‖∇S‖ = 1 satisfied by any distance function S(x). This leads to a one-to-one map between ψ(x) and S(x) and allows for recovery of S(x) from ψ(x) through an explicit mathematical relationship. Since the wave function can be regarded as a square-root density function, we are able to exploit this connection and convert shape complex distance transforms into probability density functions. Furthermore, square-root density functions can be seen as points on a unit hypersphere whose Riemannian structure is fully known. A shape complex atlas is constructed by first computing the Karcher mean ψ̄(x) of the wave functions, followed by an inverse mapping of the estimated mean back to the space of distance transforms in order to realize the atlas. We demonstrate the shape complex atlas computation via a set of experiments on a population of brain MRI scans. We also present modes of variation from the computed atlas for the control population to demonstrate the shape complex variability. PMID:20879384

  6. Construction of neuroanatomical shape complex atlas from 3D brain MRI.

    PubMed

    Chen, Ting; Rangarajan, Anand; Eisenschenk, Stephan J; Vemuri, Baba C

    2010-01-01

    This paper proposes a novel technique for constructing a neuroanatomical shape complex atlas using an information geometry framework. A shape complex is a collection of shapes in a local neighborhood. We represent the boundary of the entire shape complex using the zero level set of a distance function S(x). The spatial relations between the different anatomical structures constituting the shape complex are captured via the distance transform. We then leverage the well known relationship between the stationary state wave function psi(x) of the Schrödinger equation -h2nabla2 psi + psi = 0 and the eikonal equation //nablaS// = 1 satisfied by any distance function S(x). This leads to a one-to-one map between psi(x) and S(x) and allows for recovery of S(x) from psi(x) through an explicit mathematical relationship. Since the wave function can be regarded as a square-root density function, we are able to exploit this connection and convert shape complex distance transforms into probability density functions. Furthermore, square-root density functions can be seen as points on a unit hypersphere whose Riemannian structure is fully known. A shape complex atlas is constructed by first computing the Karcher mean psi(x) of the wave functions, followed by an inverse mapping of the estimated mean back to the space of distance transforms in order to realize the atlas. We demonstrate the shape complex atlas computation via a set of experiments on a population of brain MRI scans. We also present modes of variation from the computed atlas for the control population to demonstrate the shape complex variability. PMID:20879384

  7. Nonlocal atlas-guided multi-channel forest learning for human brain labeling

    PubMed Central

    Ma, Guangkai; Gao, Yaozong; Wu, Guorong; Wu, Ligang; Shen, Dinggang

    2016-01-01

    Purpose: It is important for many quantitative brain studies to label meaningful anatomical regions in MR brain images. However, due to high complexity of brain structures and ambiguous boundaries between different anatomical regions, the anatomical labeling of MR brain images is still quite a challenging task. In many existing label fusion methods, appearance information is widely used. However, since local anatomy in the human brain is often complex, the appearance information alone is limited in characterizing each image point, especially for identifying the same anatomical structure across different subjects. Recent progress in computer vision suggests that the context features can be very useful in identifying an object from a complex scene. In light of this, the authors propose a novel learning-based label fusion method by using both low-level appearance features (computed from the target image) and high-level context features (computed from warped atlases or tentative labeling maps of the target image). Methods: In particular, the authors employ a multi-channel random forest to learn the nonlinear relationship between these hybrid features and target labels (i.e., corresponding to certain anatomical structures). Specifically, at each of the iterations, the random forest will output tentative labeling maps of the target image, from which the authors compute spatial label context features and then use in combination with original appearance features of the target image to refine the labeling. Moreover, to accommodate the high inter-subject variations, the authors further extend their learning-based label fusion to a multi-atlas scenario, i.e., they train a random forest for each atlas and then obtain the final labeling result according to the consensus of results from all atlases. Results: The authors have comprehensively evaluated their method on both public LONI_LBPA40 and IXI datasets. To quantitatively evaluate the labeling accuracy, the authors use the

  8. Accurate Learning with Few Atlases (ALFA): an algorithm for MRI neonatal brain extraction and comparison with 11 publicly available methods

    PubMed Central

    Serag, Ahmed; Blesa, Manuel; Moore, Emma J.; Pataky, Rozalia; Sparrow, Sarah A.; Wilkinson, A. G.; Macnaught, Gillian; Semple, Scott I.; Boardman, James P.

    2016-01-01

    Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases ‘uniformly’ distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course. PMID:27010238

  9. Accurate Learning with Few Atlases (ALFA): an algorithm for MRI neonatal brain extraction and comparison with 11 publicly available methods.

    PubMed

    Serag, Ahmed; Blesa, Manuel; Moore, Emma J; Pataky, Rozalia; Sparrow, Sarah A; Wilkinson, A G; Macnaught, Gillian; Semple, Scott I; Boardman, James P

    2016-01-01

    Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases 'uniformly' distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course. PMID:27010238

  10. Accurate Learning with Few Atlases (ALFA): an algorithm for MRI neonatal brain extraction and comparison with 11 publicly available methods

    NASA Astrophysics Data System (ADS)

    Serag, Ahmed; Blesa, Manuel; Moore, Emma J.; Pataky, Rozalia; Sparrow, Sarah A.; Wilkinson, A. G.; MacNaught, Gillian; Semple, Scott I.; Boardman, James P.

    2016-03-01

    Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases ‘uniformly’ distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course.

  11. A digital interactive human brain atlas based on Chinese visible human datasets for anatomy teaching.

    PubMed

    Li, Qiyu; Ran, Xu; Zhang, Shaoxiang; Tan, Liwen; Qiu, Mingguo

    2014-01-01

    As we know, the human brain is one of the most complicated organs in the human body, which is the key and difficult point in neuroanatomy and sectional anatomy teaching. With the rapid development and extensive application of imaging technology in clinical diagnosis, doctors are facing higher and higher requirement on their anatomy knowledge. Thus, to cultivate medical students to meet the needs of medical development today and to improve their ability to read and understand radiographic images have become urgent challenges for the medical teachers. In this context, we developed a digital interactive human brain atlas based on the Chinese visible human datasets for anatomy teaching (available for free download from http://www.chinesevisiblehuman.com/down/DHBA.rar). The atlas simultaneously provides views in all 3 primary planes of section. The main structures of the human brain have been anatomically labeled in all 3 views. It is potentially useful for anatomy browsing, user self-testing, and automatic student assessment. In a word, it is interactive, 3D, user friendly, and free of charge, which can provide a new, intuitive means for anatomy teaching. PMID:24336036

  12. 4D MEMRI atlas of neonatal FVB/N mouse brain development.

    PubMed

    Szulc, Kamila U; Lerch, Jason P; Nieman, Brian J; Bartelle, Benjamin B; Friedel, Miriam; Suero-Abreu, Giselle A; Watson, Charles; Joyner, Alexandra L; Turnbull, Daniel H

    2015-09-01

    The widespread use of the mouse as a model system to study brain development has created the need for noninvasive neuroimaging methods that can be applied to early postnatal mice. The goal of this study was to optimize in vivo three- (3D) and four-dimensional (4D) manganese (Mn)-enhanced MRI (MEMRI) approaches for acquiring and analyzing data from the developing mouse brain. The combination of custom, stage-dependent holders and self-gated (motion-correcting) 3D MRI sequences enabled the acquisition of high-resolution (100-μm isotropic), motion artifact-free brain images with a high level of contrast due to Mn-enhancement of numerous brain regions and nuclei. We acquired high-quality longitudinal brain images from two groups of FVB/N strain mice, six mice per group, each mouse imaged on alternate odd or even days (6 3D MEMRI images at each day) covering the developmental stages between postnatal days 1 to 11. The effects of Mn-exposure, anesthesia and MRI were assessed, showing small but significant transient effects on body weight and brain volume, which recovered with time and did not result in significant morphological differences when compared to controls. Metrics derived from deformation-based morphometry (DBM) were used for quantitative analysis of changes in volume and position of a number of brain regions. The cerebellum, a brain region undergoing significant changes in size and patterning at early postnatal stages, was analyzed in detail to demonstrate the spatiotemporal characterization made possible by this new atlas of mouse brain development. These results show that MEMRI is a powerful tool for quantitative analysis of mouse brain development, with great potential for in vivo phenotype analysis in mouse models of neurodevelopmental diseases. PMID:26037053

  13. Quantitative map of multiple auditory cortical regions with a stereotaxic fine-scale atlas of the mouse brain

    PubMed Central

    Tsukano, Hiroaki; Horie, Masao; Hishida, Ryuichi; Takahashi, Kuniyuki; Takebayashi, Hirohide; Shibuki, Katsuei

    2016-01-01

    Optical imaging studies have recently revealed the presence of multiple auditory cortical regions in the mouse brain. We have previously demonstrated, using flavoprotein fluorescence imaging, at least six regions in the mouse auditory cortex, including the anterior auditory field (AAF), primary auditory cortex (AI), the secondary auditory field (AII), dorsoanterior field (DA), dorsomedial field (DM), and dorsoposterior field (DP). While multiple regions in the visual cortex and somatosensory cortex have been annotated and consolidated in recent brain atlases, the multiple auditory cortical regions have not yet been presented from a coronal view. In the current study, we obtained regional coordinates of the six auditory cortical regions of the C57BL/6 mouse brain and illustrated these regions on template coronal brain slices. These results should reinforce the existing mouse brain atlases and support future studies in the auditory cortex. PMID:26924462

  14. Allene ether Nazarov cyclization.

    PubMed

    Tius, Marcus A

    2014-05-01

    The ease of synthesis and the exceptional reactivity of alkoxyallenes has led to their use in a large number of highly diverse applications. This Report describes their use in various versions of the allene ether Nazarov cyclization. Following a brief introduction to the Nazarov cyclization (Section 1), the oxidative cyclization of vinyl alkoxyallenes is discussed first (Section 2). Nazarov cyclizations of α-alkoxyallenyl vinyl ketones and of α-alkoxyallenyl vinyl tertiary carbinols are covered (Section 3). The discovery and the subsequent rational design of acetals that serve as chiral auxiliaries on the allene in highly enantioselective Nazarov cyclizations is explained (Section 4). Interrupted Nazarov cyclizations of alkoxyallenes that are generated in situ from the isomerization of propargyl ethers on solid supports are discussed, including the evolution of a highly diastereoselective, chiral auxiliary controlled version of the reaction. Some applications of the methodology to natural products total synthesis have been included so as to provide the reader with benchmarks with which to judge the utility of the methodology. PMID:24196585

  15. Multi-Contrast Multi-Atlas Parcellation of Diffusion Tensor Imaging of the Human Brain

    PubMed Central

    Tang, Xiaoying; Yoshida, Shoko; Hsu, John; Huisman, Thierry A. G. M.; Faria, Andreia V.; Oishi, Kenichi; Kutten, Kwame; Poretti, Andrea; Li, Yue; Miller, Michael I.; Mori, Susumu

    2014-01-01

    In this paper, we propose a novel method for parcellating the human brain into 193 anatomical structures based on diffusion tensor images (DTIs). This was accomplished in the setting of multi-contrast diffeomorphic likelihood fusion using multiple DTI atlases. DTI images are modeled as high dimensional fields, with each voxel exhibiting a vector valued feature comprising of mean diffusivity (MD), fractional anisotropy (FA), and fiber angle. For each structure, the probability distribution of each element in the feature vector is modeled as a mixture of Gaussians, the parameters of which are estimated from the labeled atlases. The structure-specific feature vector is then used to parcellate the test image. For each atlas, a likelihood is iteratively computed based on the structure-specific vector feature. The likelihoods from multiple atlases are then fused. The updating and fusing of the likelihoods is achieved based on the expectation-maximization (EM) algorithm for maximum a posteriori (MAP) estimation problems. We first demonstrate the performance of the algorithm by examining the parcellation accuracy of 18 structures from 25 subjects with a varying degree of structural abnormality. Dice values ranging 0.8–0.9 were obtained. In addition, strong correlation was found between the volume size of the automated and the manual parcellation. Then, we present scan-rescan reproducibility based on another dataset of 16 DTI images – an average of 3.73%, 1.91%, and 1.79% for volume, mean FA, and mean MD respectively. Finally, the range of anatomical variability in the normal population was quantified for each structure. PMID:24809486

  16. Accelerated detection of intracranial space-occupying lesions with CUDA based on statistical texture atlas in brain HRCT.

    PubMed

    Liu, Wei; Feng, Huanqing; Li, Chuanfu; Huang, Yufeng; Wu, Dehuang; Tong, Tong

    2009-01-01

    In this paper, we present a method that detects intracranial space-occupying lesions in two-dimensional (2D) brain high-resolution CT images. Use of statistical texture atlas technique localizes anatomy variation in the gray level distribution of brain images, and in turn, identifies the regions with lesions. The statistical texture atlas involves 147 HRCT slices of normal individuals and its construction is extremely time-consuming. To improve the performance of atlas construction, we have implemented the pixel-wise texture extraction procedure on Nvidia 8800GTX GPU with Compute Unified Device Architecture (CUDA) platform. Experimental results indicate that the extracted texture feature is distinctive and robust enough, and is suitable for detecting uniform and mixed density space-occupying lesions. In addition, a significant speedup against straight forward CPU version was achieved with CUDA. PMID:19963990

  17. The INIA19 Template and NeuroMaps Atlas for Primate Brain Image Parcellation and Spatial Normalization

    PubMed Central

    Rohlfing, Torsten; Kroenke, Christopher D.; Sullivan, Edith V.; Dubach, Mark F.; Bowden, Douglas M.; Grant, Kathleen A.; Pfefferbaum, Adolf

    2012-01-01

    The INIA19 is a new, high-quality template for imaging-based studies of non-human primate brains, created from high-resolution, T1-weighted magnetic resonance (MR) images of 19 rhesus macaque (Macaca mulatta) animals. Combined with the comprehensive cortical and sub-cortical label map of the NeuroMaps atlas, the INIA19 is equally suitable for studies requiring both spatial normalization and atlas label propagation. Population-averaged template images are provided for both the brain and the whole head, to allow alignment of the atlas with both skull-stripped and unstripped data, and thus to facilitate its use for skull stripping of new images. This article describes the construction of the template using freely available software tools, as well as the template itself, which is being made available to the scientific community (http://nitrc.org/projects/inia19/). PMID:23230398

  18. A human brain atlas derived via n-cut parcellation of resting-state and task-based fMRI data.

    PubMed

    James, George Andrew; Hazaroglu, Onder; Bush, Keith A

    2016-02-01

    The growth of functional MRI has led to development of human brain atlases derived by parcellating resting-state connectivity patterns into functionally independent regions of interest (ROIs). All functional atlases to date have been derived from resting-state fMRI data. But given that functional connectivity between regions varies with task, we hypothesized that an atlas incorporating both resting-state and task-based fMRI data would produce an atlas with finer characterization of task-relevant regions than an atlas derived from resting-state alone. To test this hypothesis, we derived parcellation atlases from twenty-nine healthy adult participants enrolled in the Cognitive Connectome project, an initiative to improve functional MRI's translation into clinical decision-making by mapping normative variance in brain-behavior relationships. Participants underwent resting-state and task-based fMRI spanning nine cognitive domains: motor, visuospatial, attention, language, memory, affective processing, decision-making, working memory, and executive function. Spatially constrained n-cut parcellation derived brain atlases using (1) all participants' functional data (Task) or (2) a single resting-state scan (Rest). An atlas was also derived from random parcellation for comparison purposes (Random). Two methods were compared: (1) a parcellation applied to the group's mean edge weights (mean), and (2) a two-stage approach with parcellation of individual edge weights followed by parcellation of mean binarized edges (two-stage). The resulting Task and Rest atlases had significantly greater similarity with each other (mean Jaccard indices JI=0.72-0.85) than with the Random atlases (JI=0.59-0.63; all p<0.001 after Bonferroni correction). Task and Rest atlas similarity was greatest for the two-stage method (JI=0.85), which has been shown as more robust than the mean method; these atlases also better reproduced voxelwise seed maps of the left dorsolateral prefrontal cortex during

  19. A mesoscale connectome of the mouse brain.

    PubMed

    Oh, Seung Wook; Harris, Julie A; Ng, Lydia; Winslow, Brent; Cain, Nicholas; Mihalas, Stefan; Wang, Quanxin; Lau, Chris; Kuan, Leonard; Henry, Alex M; Mortrud, Marty T; Ouellette, Benjamin; Nguyen, Thuc Nghi; Sorensen, Staci A; Slaughterbeck, Clifford R; Wakeman, Wayne; Li, Yang; Feng, David; Ho, Anh; Nicholas, Eric; Hirokawa, Karla E; Bohn, Phillip; Joines, Kevin M; Peng, Hanchuan; Hawrylycz, Michael J; Phillips, John W; Hohmann, John G; Wohnoutka, Paul; Gerfen, Charles R; Koch, Christof; Bernard, Amy; Dang, Chinh; Jones, Allan R; Zeng, Hongkui

    2014-04-10

    Comprehensive knowledge of the brain's wiring diagram is fundamental for understanding how the nervous system processes information at both local and global scales. However, with the singular exception of the C. elegans microscale connectome, there are no complete connectivity data sets in other species. Here we report a brain-wide, cellular-level, mesoscale connectome for the mouse. The Allen Mouse Brain Connectivity Atlas uses enhanced green fluorescent protein (EGFP)-expressing adeno-associated viral vectors to trace axonal projections from defined regions and cell types, and high-throughput serial two-photon tomography to image the EGFP-labelled axons throughout the brain. This systematic and standardized approach allows spatial registration of individual experiments into a common three dimensional (3D) reference space, resulting in a whole-brain connectivity matrix. A computational model yields insights into connectional strength distribution, symmetry and other network properties. Virtual tractography illustrates 3D topography among interconnected regions. Cortico-thalamic pathway analysis demonstrates segregation and integration of parallel pathways. The Allen Mouse Brain Connectivity Atlas is a freely available, foundational resource for structural and functional investigations into the neural circuits that support behavioural and cognitive processes in health and disease. PMID:24695228

  20. Automatic Testing and Assessment of Neuroanatomy Using a Digital Brain Atlas: Method and Development of Computer- and Mobile-Based Applications

    ERIC Educational Resources Information Center

    Nowinski, Wieslaw L.; Thirunavuukarasuu, Arumugam; Ananthasubramaniam, Anand; Chua, Beng Choon; Qian, Guoyu; Nowinska, Natalia G.; Marchenko, Yevgen; Volkau, Ihar

    2009-01-01

    Preparation of tests and student's assessment by the instructor are time consuming. We address these two tasks in neuroanatomy education by employing a digital media application with a three-dimensional (3D), interactive, fully segmented, and labeled brain atlas. The anatomical and vascular models in the atlas are linked to "Terminologia…

  1. Three-dimensional interactive and stereotactic human brain atlas of white matter tracts.

    PubMed

    Nowinski, Wieslaw L; Chua, Beng Choon; Yang, Guo Liang; Qian, Guo Yu

    2012-01-01

    We present a human brain atlas of white matter (WM) tracts containing 40 major tracts, which is three-dimensional (3D), segmented, labeled, interactive, stereotactic and correlated to structure and vasculature. We consider: (1) WM accuracy by correlating WM tracts to underlying neuroanatomy and quantifying them; (2) balance between realism and completeness by processing a sequence of track volumes generated for various parameters with the increasing track number to enable a tract "shape convergence". MPRAGE and DTI in 64 directions of the same subject were acquired on 3 Tesla. The method has three steps: DTI-MPRAGE registration, 3D tract generation from DTI, to WM reconstruction from MPRAGE to parcellation into 17 components. 82 track volumes were generated for a wide spectrum of parameter values: Fractional Anisotropy threshold in [0.0125, 0.55] and trajectory angle lower than 45°, 60°, 65°, 70°, 75°, 80°, 85°, 90°. For each tract, a sequence of track volumes was processed to create/edit contours delineating this tract to achieve its shape convergence. The parcellated tracts were grouped into commissures, associations, projections and posterior fossa tracts, and labeled following Terminologia Anatomica. To facilitate that, a dedicated tract editor is developed which processes multiple track volumes, handles tracts in three representations (tracks, contours, envelopes); provides editing/visualization simultaneously on axial, coronal, sagittal planes; enables tract labeling and coloring; and provides numerous tools (track counting, smoothing and length thresholding; representation conversion and saving; structural atlas support). A stereotactic tract atlas along with parcellated WM was developed to explore in real-time any individual tract or their groups along with surrounding neuroanatomy. PMID:21505883

  2. A histology-based atlas of the C57BL/6J mouse brain deformably registered to in vivo MRI for localized radiation and surgical targeting

    NASA Astrophysics Data System (ADS)

    Purger, David; McNutt, Todd; Achanta, Pragathi; Quiñones-Hinojosa, Alfredo; Wong, John; Ford, Eric

    2009-12-01

    The C57BL/6J laboratory mouse is commonly used in neurobiological research. Digital atlases of the C57BL/6J brain have been used for visualization, genetic phenotyping and morphometry, but currently lack the ability to accurately calculate deviations between individual mice. We developed a fully three-dimensional digital atlas of the C57BL/6J brain based on the histology atlas of Paxinos and Franklin (2001 The Mouse Brain in Stereotaxic Coordinates 2nd edn (San Diego, CA: Academic)). The atlas uses triangular meshes to represent the various structures. The atlas structures can be overlaid and deformed to individual mouse MR images. For this study, we selected 18 structures from the histological atlas. Average atlases can be created for any group of mice of interest by calculating the mean three-dimensional positions of corresponding individual mesh vertices. As a validation of the atlas' accuracy, we performed deformable registration of the lateral ventricles to 13 MR brain scans of mice in three age groups: 5, 8 and 9 weeks old. Lateral ventricle structures from individual mice were compared to the corresponding average structures and the original histology structures. We found that the average structures created using our method more accurately represent individual anatomy than histology-based atlases alone, with mean vertex deviations of 0.044 mm versus 0.082 mm for the left lateral ventricle and 0.045 mm versus 0.068 mm for the right lateral ventricle. Our atlas representation gives direct spatial deviations for structures of interest. Our results indicate that MR-deformable histology-based atlases represent an accurate method to obtain accurate morphometric measurements of a population of mice, and that this method may be applied to phenotyping experiments in the future as well as precision targeting of surgical procedures or radiation treatment.

  3. A digital atlas of ion channel expression patterns in the two-week-old rat brain.

    PubMed

    Shcherbatyy, Volodymyr; Carson, James; Yaylaoglu, Murat; Jäckle, Katharina; Grabbe, Frauke; Brockmeyer, Maren; Yavuz, Halenur; Eichele, Gregor

    2015-01-01

    The approximately 350 ion channels encoded by the mammalian genome are a main pillar of the nervous system. We have determined the expression pattern of 320 channels in the two-week-old (P14) rat brain by means of non-radioactive robotic in situ hybridization. Optimized methods were developed and implemented to generate stringently coronal brain sections. The use of standardized methods permits a direct comparison of expression patterns across the entire ion channel expression pattern data set and facilitates recognizing ion channel co-expression. All expression data are made publically available at the Genepaint.org database. Inwardly rectifying potassium channels (Kir, encoded by the Kcnj genes) regulate a broad spectrum of physiological processes. Kcnj channel expression patterns generated in the present study were fitted with a deformable subdivision mesh atlas produced for the P14 rat brain. This co-registration, when combined with numerical quantification of expression strengths, allowed for semi-quantitative automated annotation of expression patterns as well as comparisons among and between Kcnj subfamilies. The expression patterns of Kcnj channel were also cross validated against previously published expression patterns of Kcnj channel genes. PMID:25284011

  4. Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Bower, Geoffrey

    2007-05-01

    The Allen Telescope Array (ATA) is a pioneering centimeter-wavelength radio telescope that will produce science that cannot be done with any other instrument. The ATA is the first radio telescope designed for commensal observing; it will undertake the most comprehensive and sensitive SETI surveys ever done as well as the deepest and largest area continuum and spectroscopic surveys. Science operations will commence this year with a 42-element array. The ATA will ultimately comprise 350 6-meter dishes at Hat Creek in California, and will make possible large, deep radio surveys that were not previously feasible. The telescope incorporates many new design features including hydroformed antenna surfaces, a log-periodic feed covering the entire range of frequencies from 500 MHz to 11.2 GHz, low noise, wide-band amplifiers with a flat response over the entire band. The full array has the sensitivity of the Very Large Array but with a survey capability that is greater by an order of magnitude due to the wide field of view of the 6-meter dishes. Even with 42 elements, the ATA will be one of the most powerful radio survey telescopes. Science goals include the Five GHz sky survey (FiGSS) to match the 1.4-GHz NRAO VLA Sky Survey (NVSS) and the Sloan Digital Sky Survey within the first year of operation with the 42 element array, and a deep all-sky survey of extragalactic hydrogen to investigate galaxy evolution and intergalactic gas accretion. Transient and variable source surveys, pulsar science, spectroscopy of new molecular species in the galaxy, large-scale mapping of galactic magnetic filaments, and wide-field imaging of comets and other solar system objects are among the other key science objectives of the ATA. SETI surveys will reach sufficient sensitivity to detect an Arecibo planetary radar from 1,000,000 stars to distances of 300 pc.

  5. A histology-based atlas of the C57BL/6J mouse brain deformably registered to in vivo MRI for localized radiation and surgical targeting

    PubMed Central

    Purger, David; McNutt, Todd; Achanta, Pragathi; Quiñones-Hinojosa, Alfredo; Wong, John; Ford, Eric

    2011-01-01

    The C57BL/6J laboratory mouse is commonly used in neurobiological research. Digital atlases of the C57BL/6J brain have been used for visualization, genetic phenotyping and morphometry, but currently lack the ability to accurately calculate deviations between individual mice. We developed a fully three-dimensional digital atlas of the C57BL/6J brain based on the histology atlas of Paxinos and Franklin (2001 The Mouse Brain in Stereotaxic Coordinates 2nd edn (San Diego, CA: Academic)). The atlas uses triangular meshes to represent the various structures. The atlas structures can be overlaid and deformed to individual mouse MR images. For this study, we selected 18 structures from the histological atlas. Average atlases can be created for any group of mice of interest by calculating the mean three-dimensional positions of corresponding individual mesh vertices. As a validation of the atlas’ accuracy, we performed deformable registration of the lateral ventricles to 13 MR brain scans of mice in three age groups: 5, 8 and 9 weeks old. Lateral ventricle structures from individual mice were compared to the corresponding average structures and the original histology structures. We found that the average structures created using our method more accurately represent individual anatomy than histology-based atlases alone, with mean vertex deviations of 0.044 mm versus 0.082 mm for the left lateral ventricle and 0.045 mm versus 0.068 mm for the right lateral ventricle. Our atlas representation gives direct spatial deviations for structures of interest. Our results indicate that MR-deformable histology-based atlases represent an accurate method to obtain accurate morphometric measurements of a population of mice, and that this method may be applied to phenotyping experiments in the future as well as precision targeting of surgical procedures or radiation treatment. PMID:19926915

  6. Statistical model of laminar structure for atlas-based segmentation of the fetal brain from in utero MR images

    NASA Astrophysics Data System (ADS)

    Habas, Piotr A.; Kim, Kio; Chandramohan, Dharshan; Rousseau, Francois; Glenn, Orit A.; Studholme, Colin

    2009-02-01

    Recent advances in MR and image analysis allow for reconstruction of high-resolution 3D images from clinical in utero scans of the human fetal brain. Automated segmentation of tissue types from MR images (MRI) is a key step in the quantitative analysis of brain development. Conventional atlas-based methods for adult brain segmentation are limited in their ability to accurately delineate complex structures of developing tissues from fetal MRI. In this paper, we formulate a novel geometric representation of the fetal brain aimed at capturing the laminar structure of developing anatomy. The proposed model uses a depth-based encoding of tissue occurrence within the fetal brain and provides an additional anatomical constraint in a form of a laminar prior that can be incorporated into conventional atlas-based EM segmentation. Validation experiments are performed using clinical in utero scans of 5 fetal subjects at gestational ages ranging from 20.5 to 22.5 weeks. Experimental results are evaluated against reference manual segmentations and quantified in terms of Dice similarity coefficient (DSC). The study demonstrates that the use of laminar depth-encoded tissue priors improves both the overall accuracy and precision of fetal brain segmentation. Particular refinement is observed in regions of the parietal and occipital lobes where the DSC index is improved from 0.81 to 0.82 for cortical grey matter, from 0.71 to 0.73 for the germinal matrix, and from 0.81 to 0.87 for white matter.

  7. Evidence for potentials and limitations of brain plasticity using an atlas of functional resectability of WHO grade II gliomas: towards a "minimal common brain".

    PubMed

    Ius, Tamara; Angelini, Elsa; Thiebaut de Schotten, Michel; Mandonnet, Emmanuel; Duffau, Hugues

    2011-06-01

    Despite recent advances in non-invasive brain mapping imaging, the resectability of a given area in a patient harboring a WHO grade II glioma cannot be predicted preoperatively with high reliability, due to mechanisms of functional reorganization. Therefore, intraoperative mapping by direct electrical stimulation remains the gold standard for detection and preservation of eloquent areas during glioma surgery, because it enables to perform on-line anatomo-functional correlations. To study potentials and limitations of brain plasticity, we gathered 58 postoperative MRI of patients operated on for a WHO grade II glioma under direct electrical cortico-subcortical stimulation. Postoperative images were registered on the MNI template to construct an atlas of functional resectability for which each voxel represents the probability to observe residual non-resectable tumor, that is, non-compensable area. The resulting atlas offers a rigorous framework to identify areas with high plastic potential (i.e. with probabilities of residual tumor close to 0), with low compensatory capabilities (i.e. probabilities of residual tumor close to 1) and with intermediate level of resectability (probability around 0.5). The resulting atlas highlights the utmost importance of preserving a core of connectivity through the main associative pathways, namely, it supports the existence of a "minimal common brain" among patients. PMID:21414413

  8. Cell-type–based model explaining coexpression patterns of genes in the brain

    PubMed Central

    Grange, Pascal; Bohland, Jason W.; Okaty, Benjamin W.; Sugino, Ken; Bokil, Hemant; Nelson, Sacha B.; Ng, Lydia; Hawrylycz, Michael; Mitra, Partha P.

    2014-01-01

    Spatial patterns of gene expression in the vertebrate brain are not independent, as pairs of genes can exhibit complex patterns of coexpression. Two genes may be similarly expressed in one region, but differentially expressed in other regions. These correlations have been studied quantitatively, particularly for the Allen Atlas of the adult mouse brain, but their biological meaning remains obscure. We propose a simple model of the coexpression patterns in terms of spatial distributions of underlying cell types and establish its plausibility using independently measured cell-type–specific transcriptomes. The model allows us to predict the spatial distribution of cell types in the mouse brain. PMID:24706869

  9. Improving the quantitative accuracy of cerebral oxygen saturation in monitoring the injured brain using atlas based Near Infrared Spectroscopy models.

    PubMed

    Clancy, Michael; Belli, Antonio; Davies, David; Lucas, Samuel J E; Su, Zhangjie; Dehghani, Hamid

    2016-08-01

    The application of Near Infrared Spectroscopy (NIRS) for the monitoring of the cerebral oxygen saturation within the brain is well established, albeit using temporal data that can only measure relative changes of oxygenation state of the brain from a baseline. The focus of this investigation is to demonstrate that hybridisation of existing near infrared probe designs and reconstruction techniques can pave the way to produce a system and methods that can be used to monitor the absolute oxygen saturation in the injured brain. Using registered Atlas models in simulation, a novel method is outlined by which the quantitative accuracy and practicality of NIRS for specific use in monitoring the injured brain, can be improved, with cerebral saturation being recovered to within 10.1 ± 1.8% of the expected values. PMID:27003677

  10. Allene Functionalization via Bicyclic Methylene Aziridines

    PubMed Central

    Boralsky, Luke A.; Marston, Dagmara; Grigg, R. David; Hershberger, John C.; Schomaker, Jennifer M.

    2011-01-01

    The oxidative functionalization of olefins is a common method for the formation of vicinal carbon-heteroatom bonds. However, oxidative methods to transform allenes into synthetic motifs containing three contiguous carbon-heteroatom bonds are much less developed. This paper describes the use of bicyclic methylene aziridines (MAs), prepared via intramolecular allene aziridination, as scaffolds for functionalization of all three allene carbons. PMID:21438516

  11. A spatio-temporal latent atlas for semi-supervised learning of fetal brain segmentations and morphological age estimation.

    PubMed

    Dittrich, Eva; Riklin Raviv, Tammy; Kasprian, Gregor; Donner, René; Brugger, Peter C; Prayer, Daniela; Langs, Georg

    2014-01-01

    Prenatal neuroimaging requires reference models that reflect the normal spectrum of fetal brain development, and summarize observations from a representative sample of individuals. Collecting a sufficiently large data set of manually annotated data to construct a comprehensive in vivo atlas of rapidly developing structures is challenging but necessary for large population studies and clinical application. We propose a method for the semi-supervised learning of a spatio-temporal latent atlas of fetal brain development, and corresponding segmentations of emerging cerebral structures, such as the ventricles or cortex. The atlas is based on the annotation of a few examples, and a large number of imaging data without annotation. It models the morphological and developmental variability across the population. Furthermore, it serves as basis for the estimation of a structures' morphological age, and its deviation from the nominal gestational age during the assessment of pathologies. Experimental results covering the gestational period of 20-30 gestational weeks demonstrate segmentation accuracy achievable with minimal annotation, and precision of morphological age estimation. Age estimation results on fetuses suffering from lissencephaly demonstrate that they detect significant differences in the age offset compared to a control group. PMID:24080527

  12. Anatomo-clinical atlases correlate clinical data and electrode contact coordinates: application to subthalamic deep brain stimulation.

    PubMed

    Lalys, Florent; Haegelen, Claire; Mehri, Maroua; Drapier, Sophie; Vérin, Marc; Jannin, Pierre

    2013-01-30

    For patients suffering from Parkinson's disease with severe movement disorders, functional surgery may be required when medical therapy is not effective. In Deep Brain Stimulation (DBS), electrodes are implanted within the brain to stimulate deep structures such as SubThalamic Nucleus (STN). The quality of patient surgical outcome is generally related to the accuracy of nucleus targeting during surgery. In this paper, we focused on identifying optimum sites for STN DBS by studying symptomatic motor improvement along with neuropsychological side effects. We described successive steps for constructing digital atlases gathering patient's location of electrode contacts automatically segmented from postoperative images, and clinical scores. Three motor and five neuropsychological scores were included in the study. Correlations with active contact locations were carried out using an adapted hierarchical ascendant classification. Such analysis enabled the extraction of representative clusters to determine the optimum site for therapeutic STN DBS. For each clinical score, we built an anatomo-clinical atlas representing its improvement or deterioration in relation with the anatomical location of electrodes and from a population of implanted patients. To the best of our knowledge, we reported for the first time a discrepancy between a very good motor improvement by targeting the postero-superior region of the STN and an inevitable deterioration of the categorical and phonemic fluency in the same region. Such atlases and associated analysis may help better understanding of functional mapping in deep structures and may help pre-operative decision-making process and especially targeting. PMID:23147008

  13. A Critique of Mark D. Allen's "The Preservation of Verb Subcategory Knowledge in a Spoken Language Comprehension Deficit"

    ERIC Educational Resources Information Center

    Kemmerer, David

    2008-01-01

    Allen [Allen, M. (2005). "The preservation of verb subcategory knowledge in a spoken language comprehension deficit." "Brain and Language, 95", 255-264.] reports a single patient, WBN, who, during spoken language comprehension, is still able to access some of the syntactic properties of verbs despite being unable to access some of their semantic…

  14. Stereoscopic three-dimensional visualization applied to multimodal brain images: clinical applications and a functional connectivity atlas

    PubMed Central

    Rojas, Gonzalo M.; Gálvez, Marcelo; Vega Potler, Natan; Craddock, R. Cameron; Margulies, Daniel S.; Castellanos, F. Xavier; Milham, Michael P.

    2014-01-01

    Effective visualization is central to the exploration and comprehension of brain imaging data. While MRI data are acquired in three-dimensional space, the methods for visualizing such data have rarely taken advantage of three-dimensional stereoscopic technologies. We present here results of stereoscopic visualization of clinical data, as well as an atlas of whole-brain functional connectivity. In comparison with traditional 3D rendering techniques, we demonstrate the utility of stereoscopic visualizations to provide an intuitive description of the exact location and the relative sizes of various brain landmarks, structures and lesions. In the case of resting state fMRI, stereoscopic 3D visualization facilitated comprehension of the anatomical position of complex large-scale functional connectivity patterns. Overall, stereoscopic visualization improves the intuitive visual comprehension of image contents, and brings increased dimensionality to visualization of traditional MRI data, as well as patterns of functional connectivity. PMID:25414626

  15. A Digital Atlas of Middle to Large Brain Vessels and Their Relation to Cortical and Subcortical Structures

    PubMed Central

    Viviani, Roberto

    2016-01-01

    While widely distributed, the vascular supply of the brain is particularly prominent in certain anatomical structures because of the high vessel density or their large size. A digital atlas of middle to large vessels in Montreal Neurological Institute (MNI) coordinates is here presented, obtained from a sample of N = 38 healthy participants scanned with the time-of-flight (TOF) magnetic resonance technique, and normalized with procedures analogous to those commonly used in functional neuroimaging studies. Spatial colocalization of brain parenchyma and vessels is shown to affect specific structures such as the anteromedial face of the temporal lobe, the cortex surrounding the Sylvian fissure (Sy), the anterior cingular cortex, and the ventral striatum. The vascular frequency maps presented here provide objective information about the vascularization of the brain, and may assist in the interpretation of data in studies where vessels are a potential confound. PMID:26924965

  16. Generation and Disease Model Relevance of a Manganese Enhanced Magnetic Resonance Imaging-Based NOD/scid-IL-2Rγc(null) Mouse Brain Atlas.

    PubMed

    Sajja, Balasrinivasa R; Bade, Aditya N; Zhou, Biyun; Uberti, Mariano G; Gorantla, Santhi; Gendelman, Howard E; Boska, Michael D; Liu, Yutong

    2016-03-01

    Strain specific mouse brain magnetic resonance imaging (MRI) atlases provide coordinate space linked anatomical registration. This allows longitudinal quantitative analyses of neuroanatomical volumes and imaging metrics for assessing the role played by aging and disease to the central nervous system. As NOD/scid-IL-2Rγ(c)(null) (NSG) mice allow human cell transplantation to study human disease, these animals are used to assess brain morphology. Manganese enhanced MRI (MEMRI) improves contrasts amongst brain components and as such can greatly help identifying a broad number of structures on MRI. To this end, NSG adult mouse brains were imaged in vivo on a 7.0 Tesla MR scanner at an isotropic resolution of 100 μm. A population averaged brain of 19 mice was generated using an iterative alignment algorithm. MEMRI provided sufficient contrast permitting 41 brain structures to be manually labeled. Volumes of 7 humanized mice brain structures were measured by atlas-based segmentation and compared against non-humanized controls. The humanized NSG mice brain volumes were smaller than controls (p < 0.001). Many brain structures of humanized mice were significantly smaller than controls. We posit that the irradiation and cell grafting involved in the creation of humanized mice were responsible for the morphological differences. Six NSG mice without MnCl2 administration were scanned with high resolution T2-weighted MRI and segmented to test broad utility of the atlas. PMID:26556033

  17. Automated tissue classification of pediatric brains from magnetic resonance images using age-specific atlases

    NASA Astrophysics Data System (ADS)

    Metzger, Andrew; Benavides, Amanda; Nopoulos, Peg; Magnotta, Vincent

    2016-03-01

    The goal of this project was to develop two age appropriate atlases (neonatal and one year old) that account for the rapid growth and maturational changes that occur during early development. Tissue maps from this age group were initially created by manually correcting the resulting tissue maps after applying an expectation maximization (EM) algorithm and an adult atlas to pediatric subjects. The EM algorithm classified each voxel into one of ten possible tissue types including several subcortical structures. This was followed by a novel level set segmentation designed to improve differentiation between distal cortical gray matter and white matter. To minimize the req uired manual corrections, the adult atlas was registered to the pediatric scans using high -dimensional, symmetric image normalization (SyN) registration. The subject images were then mapped to an age specific atlas space, again using SyN registration, and the resulting transformation applied to the manually corrected tissue maps. The individual maps were averaged in the age specific atlas space and blurred to generate the age appropriate anatomical priors. The resulting anatomical priors were then used by the EM algorithm to re-segment the initial training set as well as an independent testing set. The results from the adult and age-specific anatomical priors were compared to the manually corrected results. The age appropriate atlas provided superior results as compared to the adult atlas. The image analysis pipeline used in this work was built using the open source software package BRAINSTools.

  18. Trans-cranial opening of the blood-brain barrier in targeted regions using a stereotaxic brain atlas and focused ultrasound energy

    PubMed Central

    2014-01-01

    Objective The blood-brain barrier (BBB) protects the brain by preventing the entry of large molecules; this poses a major obstacle for the delivery of drugs to the brain. A novel technique using focused ultrasound (FUS) energy combined with microbubble contrast agents has been widely used for non-invasive trans-cranial BBB opening. Traditionally, FUS research is conducted with magnetic resonance imaging (MRI) guidance, which is expensive and poses physical limitations due to the magnetic field. A system that could allow researchers to test brain therapies without MR intervention could facilitate and accelerate translational research. Methods In this study, we present a novel FUS system that uses a custom-built FUS generator mounted on a motorized stereotaxic apparatus with embedded brain atlas to locally open the BBB in rodents. The system was initially characterized using a tissue-mimicking phantom. Rodent studies were also performed to evaluate whether non-invasive, localized BBB opening could be achieved using brain atlas-based targeting. Brains were exposed to pulsed focused ultrasound energy at 1.06 MHz in rats and 3.23 MHz in mice, with the focal pressure estimated to be 0.5–0.6 MPa through the skull. BBB opening was confirmed in gross tissue sections by the presence of Evans blue leakage in the exposed region of the brain and by histological assessment. Results The targeting accuracy of the stereotaxic system was better than 0.5 mm in the tissue-mimicking phantom. Reproducible localized BBB opening was verified with Evans blue dye leakage in 32/33 rats and had a targeting accuracy of ±0.3 mm. The use of higher frequency exposures in mice enabled a similar precision of localized BBB opening as was observed with the low frequency in the rat model. Conclusions With this dedicated small-animal motorized stereotaxic-FUS system, we achieved accurate targeting of focused ultrasound exposures in the brain for non-invasive opening of the BBB. This system can

  19. Mapping heritability and molecular genetic associations with cortical features using probabilistic brain atlases: methods and applications to schizophrenia.

    PubMed

    Cannon, Tyrone D; Thompson, Paul M; van Erp, Theo G M; Huttunen, Matti; Lonnqvist, Jouko; Kaprio, Jaakko; Toga, Arthur W

    2006-01-01

    There is an urgent need to decipher the complex nature of genotype-phenotype relationships within the multiple dimensions of brain structure and function that are compromised in neuropsychiatric syndromes such as schizophrenia. Doing so requires sophisticated methodologies to represent population variability in neural traits and to probe their heritable and molecular genetic bases. We have recently developed and applied computational algorithms to map the heritability of, as well as genetic linkage and association to, neural features encoded using brain imaging in the context of three-dimensional (3D), populationbased, statistical brain atlases. One set of algorithms builds on our prior work using classical twin study methods to estimate heritability by fitting biometrical models for additive genetic, unique, and common environmental influences. Another set of algorithms performs regression-based (Haseman-Elston) identical-bydescent linkage analysis and genetic association analysis of DNA polymorphisms in relation to neural traits of interest in the same 3D population-based brain atlas format. We demonstrate these approaches using samples of healthy monozygotic (MZ) and dizygotic (DZ) twin pairs, as well as MZ and DZ twin pairs discordant for schizophrenia, but the methods can be generalized to other classes of relatives and to other diseases. The results confirm prior evidence of genetic influences on gray matter density in frontal brain regions. They also provide converging evidence that the chromosome 1q42 region is relevant to schizophrenia by demonstrating linkage and association of markers of the Transelin-Associated-Factor-X and Disrupted-In- Schizophrenia-1 genes with prefrontal cortical gray matter deficits in twins discordant for schizophrenia. PMID:16595856

  20. Exploration and visualization of connectivity in the adult mouse brain.

    PubMed

    Feng, David; Lau, Chris; Ng, Lydia; Li, Yang; Kuan, Leonard; Sunkin, Susan M; Dang, Chinh; Hawrylycz, Michael

    2015-02-01

    The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. All data were aligned to a common template in 3D space to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. A suite of computational tools were developed to search and visualize the projection labeling experiments, available at http://connectivity.brain-map.org. We present three use cases illustrating how these publicly-available tools can be used to perform analyses of long range brain region connectivity. The use cases make extensive use of advanced visualization tools integrated with the atlas including projection density histograms, 3D computed anterograde and retrograde projection paths, and multi-specimen projection composites. These tools offer convenient access to detailed axonal projection information in the adult mouse brain and the ability to perform data analysis and visualization of projection fields and neuroanatomy in an integrated manner. PMID:25637033

  1. Test-retest assessment of cortical activation induced by repetitive transcranial magnetic stimulation with brain atlas-guided optical topography

    NASA Astrophysics Data System (ADS)

    Tian, Fenghua; Kozel, F. Andrew; Yennu, Amarnath; Croarkin, Paul E.; McClintock, Shawn M.; Mapes, Kimberly S.; Husain, Mustafa M.; Liu, Hanli

    2012-11-01

    Repetitive transcranial magnetic stimulation (rTMS) is a technology that stimulates neurons with rapidly changing magnetic pulses with demonstrated therapeutic applications for various neuropsychiatric disorders. Functional near-infrared spectroscopy (fNIRS) is a suitable tool to assess rTMS-evoked brain responses without interference from the magnetic or electric fields generated by the TMS coil. We have previously reported a channel-wise study of combined rTMS/fNIRS on the motor and prefrontal cortices, showing a robust decrease of oxygenated hemoglobin concentration (Δ[HbO2]) at the sites of 1-Hz rTMS and the contralateral brain regions. However, the reliability of this putative clinical tool is unknown. In this study, we develop a rapid optical topography approach to spatially characterize the rTMS-evoked hemodynamic responses on a standard brain atlas. A hemispherical approximation of the brain is employed to convert the three-dimensional topography on the complex brain surface to a two-dimensional topography in the spherical coordinate system. The test-retest reliability of the combined rTMS/fNIRS is assessed using repeated measurements performed two to three days apart. The results demonstrate that the Δ[HbO2] amplitudes have moderate-to-high reliability at the group level; and the spatial patterns of the topographic images have high reproducibility in size and a moderate degree of overlap at the individual level.

  2. Individual 3D region-of-interest atlas of the human brain: knowledge-based class image analysis for extraction of anatomical objects

    NASA Astrophysics Data System (ADS)

    Wagenknecht, Gudrun; Kaiser, Hans-Juergen; Sabri, Osama; Buell, Udalrich

    2000-06-01

    After neural network-based classification of tissue types, the second step of atlas extraction is knowledge-based class image analysis to get anatomically meaningful objects. Basic algorithms are region growing, mathematical morphology operations, and template matching. A special algorithm was designed for each object. The class label of each voxel and the knowledge about the relative position of anatomical objects to each other and to the sagittal midplane of the brain can be utilized for object extraction. User interaction is only necessary to define starting, mid- and end planes for most object extractions and to determine the number of iterations for erosion and dilation operations. Extraction can be done for the following anatomical brain regions: cerebrum; cerebral hemispheres; cerebellum; brain stem; white matter (e.g., centrum semiovale); gray matter [cortex, frontal, parietal, occipital, temporal lobes, cingulum, insula, basal ganglia (nuclei caudati, putamen, thalami)]. For atlas- based quantification of functional data, anatomical objects can be convoluted with the point spread function of functional data to take into account the different resolutions of morphological and functional modalities. This method allows individual atlas extraction from MRI image data of a patient without the need of warping individual data to an anatomical or statistical MRI brain atlas.

  3. Technical and organizational considerations for the long-term maintenance and development of digital brain atlases and web-based databases.

    PubMed

    Ito, Kei

    2010-01-01

    Digital brain atlas is a kind of image database that specifically provide information about neurons and glial cells in the brain. It has various advantages that are unmatched by conventional paper-based atlases. Such advantages, however, may become disadvantages if appropriate cares are not taken. Because digital atlases can provide unlimited amount of data, they should be designed to minimize redundancy and keep consistency of the records that may be added incrementally by different staffs. The fact that digital atlases can easily be revised necessitates a system to assure that users can access previous versions that might have been cited in papers at a particular period. To inherit our knowledge to our descendants, such databases should be maintained for a very long period, well over 100 years, like printed books and papers. Technical and organizational measures to enable long-term archive should be considered seriously. Compared to the initial development of the database, subsequent efforts to increase the quality and quantity of its contents are not regarded highly, because such tasks do not materialize in the form of publications. This fact strongly discourages continuous expansion of, and external contributions to, the digital atlases after its initial launch. To solve these problems, the role of the biocurators is vital. Appreciation of the scientific achievements of the people who do not write papers, and establishment of the secure academic career path for them, are indispensable for recruiting talents for this very important job. PMID:20661458

  4. Technical and Organizational Considerations for the Long-Term Maintenance and Development of Digital Brain Atlases and Web-Based Databases

    PubMed Central

    Ito, Kei

    2010-01-01

    Digital brain atlas is a kind of image database that specifically provide information about neurons and glial cells in the brain. It has various advantages that are unmatched by conventional paper-based atlases. Such advantages, however, may become disadvantages if appropriate cares are not taken. Because digital atlases can provide unlimited amount of data, they should be designed to minimize redundancy and keep consistency of the records that may be added incrementally by different staffs. The fact that digital atlases can easily be revised necessitates a system to assure that users can access previous versions that might have been cited in papers at a particular period. To inherit our knowledge to our descendants, such databases should be maintained for a very long period, well over 100 years, like printed books and papers. Technical and organizational measures to enable long-term archive should be considered seriously. Compared to the initial development of the database, subsequent efforts to increase the quality and quantity of its contents are not regarded highly, because such tasks do not materialize in the form of publications. This fact strongly discourages continuous expansion of, and external contributions to, the digital atlases after its initial launch. To solve these problems, the role of the biocurators is vital. Appreciation of the scientific achievements of the people who do not write papers, and establishment of the secure academic career path for them, are indispensable for recruiting talents for this very important job. PMID:20661458

  5. 3D Reconstructed Cyto-, Muscarinic M2 Receptor, and Fiber Architecture of the Rat Brain Registered to the Waxholm Space Atlas.

    PubMed

    Schubert, Nicole; Axer, Markus; Schober, Martin; Huynh, Anh-Minh; Huysegoms, Marcel; Palomero-Gallagher, Nicola; Bjaalie, Jan G; Leergaard, Trygve B; Kirlangic, Mehmet E; Amunts, Katrin; Zilles, Karl

    2016-01-01

    High-resolution multiscale and multimodal 3D models of the brain are essential tools to understand its complex structural and functional organization. Neuroimaging techniques addressing different aspects of brain organization should be integrated in a reference space to enable topographically correct alignment and subsequent analysis of the various datasets and their modalities. The Waxholm Space (http://software.incf.org/software/waxholm-space) is a publicly available 3D coordinate-based standard reference space for the mapping and registration of neuroanatomical data in rodent brains. This paper provides a newly developed pipeline combining imaging and reconstruction steps with a novel registration strategy to integrate new neuroimaging modalities into the Waxholm Space atlas. As a proof of principle, we incorporated large scale high-resolution cyto-, muscarinic M2 receptor, and fiber architectonic images of rat brains into the 3D digital MRI based atlas of the Sprague Dawley rat in Waxholm Space. We describe the whole workflow, from image acquisition to reconstruction and registration of these three modalities into the Waxholm Space rat atlas. The registration of the brain sections into the atlas is performed by using both linear and non-linear transformations. The validity of the procedure is qualitatively demonstrated by visual inspection, and a quantitative evaluation is performed by measurement of the concordance between representative atlas-delineated regions and the same regions based on receptor or fiber architectonic data. This novel approach enables for the first time the generation of 3D reconstructed volumes of nerve fibers and fiber tracts, or of muscarinic M2 receptor density distributions, in an entire rat brain. Additionally, our pipeline facilitates the inclusion of further neuroimaging datasets, e.g., 3D reconstructed volumes of histochemical stainings or of the regional distributions of multiple other receptor types, into the Waxholm Space

  6. 3D Reconstructed Cyto-, Muscarinic M2 Receptor, and Fiber Architecture of the Rat Brain Registered to the Waxholm Space Atlas

    PubMed Central

    Schubert, Nicole; Axer, Markus; Schober, Martin; Huynh, Anh-Minh; Huysegoms, Marcel; Palomero-Gallagher, Nicola; Bjaalie, Jan G.; Leergaard, Trygve B.; Kirlangic, Mehmet E.; Amunts, Katrin; Zilles, Karl

    2016-01-01

    High-resolution multiscale and multimodal 3D models of the brain are essential tools to understand its complex structural and functional organization. Neuroimaging techniques addressing different aspects of brain organization should be integrated in a reference space to enable topographically correct alignment and subsequent analysis of the various datasets and their modalities. The Waxholm Space (http://software.incf.org/software/waxholm-space) is a publicly available 3D coordinate-based standard reference space for the mapping and registration of neuroanatomical data in rodent brains. This paper provides a newly developed pipeline combining imaging and reconstruction steps with a novel registration strategy to integrate new neuroimaging modalities into the Waxholm Space atlas. As a proof of principle, we incorporated large scale high-resolution cyto-, muscarinic M2 receptor, and fiber architectonic images of rat brains into the 3D digital MRI based atlas of the Sprague Dawley rat in Waxholm Space. We describe the whole workflow, from image acquisition to reconstruction and registration of these three modalities into the Waxholm Space rat atlas. The registration of the brain sections into the atlas is performed by using both linear and non-linear transformations. The validity of the procedure is qualitatively demonstrated by visual inspection, and a quantitative evaluation is performed by measurement of the concordance between representative atlas-delineated regions and the same regions based on receptor or fiber architectonic data. This novel approach enables for the first time the generation of 3D reconstructed volumes of nerve fibers and fiber tracts, or of muscarinic M2 receptor density distributions, in an entire rat brain. Additionally, our pipeline facilitates the inclusion of further neuroimaging datasets, e.g., 3D reconstructed volumes of histochemical stainings or of the regional distributions of multiple other receptor types, into the Waxholm Space

  7. H. Julian Allen: An Appreciation

    NASA Astrophysics Data System (ADS)

    Vincenti, Walter G.; Boyd, John W.; Bugos, Glenn E.

    2007-01-01

    Harvey Allen is best known as the genius behind the blunt-body concept, published in 1953, which enables spacecraft to return safely home through Earth's dense atmosphere. He was also an extraordinary research leader, who led a world-class research program in hypersonics at the NACA Ames Aeronautical Laboratory. This paper reviews his career as one of America's leading theorists and experimenters, including his engineering education at Stanford, his work on the inverse problem of calculating the airfoil profile to obtain a desired pressure distribution, his hand in constructing wind tunnels and experimental facilities at Ames, and his pioneering and wide-ranging work on atmospheric re-entry. It concludes with an appreciation of his uniquely inspirational style of research management, and of his magnetic personality.

  8. Reply to David Kemmerer's "A Critique of Mark D. Allen's "The Preservation of Verb Subcategory Knowledge in a Spoken Language Comprehension Deficit""

    ERIC Educational Resources Information Center

    Allen, Mark D.; Owens, Tyler E.

    2008-01-01

    Allen [Allen, M. D. (2005). The preservation of verb subcategory knowledge in a spoken language comprehension deficit. "Brain and Language, "95, 255-264] presents evidence from a single patient, WBN, to motivate a theory of lexical processing and representation in which syntactic information may be encoded and retrieved independently of semantic…

  9. Modular Functionalization of Allenes to Aminated Stereotriads

    PubMed Central

    Adams, Christopher S.; Boralsky, Luke A.; Guzei, Ilia A.; Schomaker, Jennifer M.

    2014-01-01

    Nitrogen-containing stereotriads- compounds with three adjacent stereodefined carbons- are commonly found in biologically important molecules. However, the preparation of molecules bearing these motifs can be challenging. Herein, we describe a modular oxidation protocol which converts a substituted allene to a triply functionalized amine of the form C-X/C-N/CY. The key step employs a Rh-catalyzed intramolecular conversion of the allene to a strained bicyclic methylene aziridine. This reactive intermediate is further elaborated to the target products, often in one reaction vessel and with effective transfer of the axial chirality of the allene to point chirality in the stereotriad. PMID:22708990

  10. [2+2+1] cyclization of allenes.

    PubMed

    Kitagaki, S; Inagaki, F; Mukai, C

    2014-05-01

    The [2+2+1] cyclization of an alkyne, an alkene and carbon monoxide, i.e., the Pauson-Khand reaction, is one of the most powerful tools for constructing a five-membered ring. In place of the alkene or alkyne part, the use of an allene functionality has proven to make this reaction more valuable for organic synthesis. This review focuses on the origin and progress of the allenic [2+2+1] cyclocarbonylation, including the chirality transfer of the allene and its synthetic applications. PMID:24514744

  11. Automatic testing and assessment of neuroanatomy using a digital brain atlas: method and development of computer- and mobile-based applications.

    PubMed

    Nowinski, Wieslaw L; Thirunavuukarasuu, Arumugam; Ananthasubramaniam, Anand; Chua, Beng Choon; Qian, Guoyu; Nowinska, Natalia G; Marchenko, Yevgen; Volkau, Ihar

    2009-10-01

    Preparation of tests and student's assessment by the instructor are time consuming. We address these two tasks in neuroanatomy education by employing a digital media application with a three-dimensional (3D), interactive, fully segmented, and labeled brain atlas. The anatomical and vascular models in the atlas are linked to Terminologia Anatomica. Because the cerebral models are fully segmented and labeled, our approach enables automatic and random atlas-derived generation of questions to test location and naming of cerebral structures. This is done in four steps: test individualization by the instructor, test taking by the students at their convenience, automatic student assessment by the application, and communication of the individual assessment to the instructor. A computer-based application with an interactive 3D atlas and a preliminary mobile-based application were developed to realize this approach. The application works in two test modes: instructor and student. In the instructor mode, the instructor customizes the test by setting the scope of testing and student performance criteria, which takes a few seconds. In the student mode, the student is tested and automatically assessed. Self-testing is also feasible at any time and pace. Our approach is automatic both with respect to test generation and student assessment. It is also objective, rapid, and customizable. We believe that this approach is novel from computer-based, mobile-based, and atlas-assisted standpoints. PMID:19743409

  12. Van Allen Discovery Most Important

    NASA Technical Reports Server (NTRS)

    Jastrow, R.

    1959-01-01

    The first step toward the exploration of space occurred approximately 22 months ago as a part of the International Geophysical Year. In the short interval since October, 1957, the new tools of research, the satellite and the space rocket, have produced two unexpected results of fundamental scientific importance. First, instruments placed in the Explorer satellites by James A. Van Allen have revealed the existence of layers of energetic particles in the outer atmosphere. This discovery constitutes the most significant research achievement of the IGY satellite program. The layers may provide the explanation for the aurora and other geophysical phenomena, and they will also influence the design of vehicles for manned space flight, whose occupants must be shielded against their harmful biological effects. Second, the shape of the earth has been determined very accurately with the aid of data from the first Vanguard. As a result of this investigation, we have found that our planet tends toward the shape of a pear, with its stem at the North Pole. This discovery may produce major changes in our ideas on the interior structure of the earth.

  13. Individual 3D region-of-interest atlas of the human brain: automatic training point extraction for neural-network-based classification of brain tissue types

    NASA Astrophysics Data System (ADS)

    Wagenknecht, Gudrun; Kaiser, Hans-Juergen; Obladen, Thorsten; Sabri, Osama; Buell, Udalrich

    2000-04-01

    Individual region-of-interest atlas extraction consists of two main parts: T1-weighted MRI grayscale images are classified into brain tissues types (gray matter (GM), white matter (WM), cerebrospinal fluid (CSF), scalp/bone (SB), background (BG)), followed by class image analysis to define automatically meaningful ROIs (e.g., cerebellum, cerebral lobes, etc.). The purpose of this algorithm is the automatic detection of training points for neural network-based classification of brain tissue types. One transaxial slice of the patient data set is analyzed. Background separation is done by simple region growing. A random generator extracts spatially uniformly distributed training points of class BG from that region. For WM training point extraction (TPE), the homogeneity operator is the most important. The most homogeneous voxels define the region for WM TPE. They are extracted by analyzing the cumulative histogram of the homogeneity operator response. Assuming a Gaussian gray value distribution in WM, a random number is used as a probabilistic threshold for TPE. Similarly, non-white matter and non-background regions are analyzed for GM and CSF training points. For SB TPE, the distance from the BG region is an additional feature. Simulated and real 3D MRI images are analyzed and error rates for TPE and classification calculated.

  14. Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas1,2,3

    PubMed Central

    Borg, Jana Schaich; Vu, Mai-Anh; Badea, Cristian; Badea, Alexandra; Johnson, G. Allan

    2015-01-01

    Abstract Simultaneous neural recordings taken from multiple areas of the rodent brain are garnering growing interest because of the insight they can provide about spatially distributed neural circuitry. The promise of such recordings has inspired great progress in methods for surgically implanting large numbers of metal electrodes into intact rodent brains. However, methods for localizing the precise location of these electrodes have remained severely lacking. Traditional histological techniques that require slicing and staining of physical brain tissue are cumbersome and become increasingly impractical as the number of implanted electrodes increases. Here we solve these problems by describing a method that registers 3D computed tomography (CT) images of intact rat brains implanted with metal electrode bundles to a magnetic resonance imaging histology (MRH) atlas. Our method allows accurate visualization of each electrode bundle’s trajectory and location without removing the electrodes from the brain or surgically implanting external markers. In addition, unlike physical brain slices, once the 3D images of the electrode bundles and the MRH atlas are registered, it is possible to verify electrode placements from many angles by “reslicing” the images along different planes of view. Furthermore, our method can be fully automated and easily scaled to applications with large numbers of specimens. Our digital imaging approach to efficiently localizing metal electrodes offers a substantial addition to currently available methods, which, in turn, may help accelerate the rate at which insights are gleaned from rodent network neuroscience. PMID:26322331

  15. NeuroVault.org: A repository for sharing unthresholded statistical maps, parcellations, and atlases of the human brain.

    PubMed

    Gorgolewski, Krzysztof J; Varoquaux, Gael; Rivera, Gabriel; Schwartz, Yannick; Sochat, Vanessa V; Ghosh, Satrajit S; Maumet, Camille; Nichols, Thomas E; Poline, Jean-Baptiste; Yarkoni, Tal; Margulies, Daniel S; Poldrack, Russell A

    2016-01-01

    NeuroVault.org is dedicated to storing outputs of analyses in the form of statistical maps, parcellations and atlases, a unique strategy that contrasts with most neuroimaging repositories that store raw acquisition data or stereotaxic coordinates. Such maps are indispensable for performing meta-analyses, validating novel methodology, and deciding on precise outlines for regions of interest (ROIs). NeuroVault is open to maps derived from both healthy and clinical populations, as well as from various imaging modalities (sMRI, fMRI, EEG, MEG, PET, etc.). The repository uses modern web technologies such as interactive web-based visualization, cognitive decoding, and comparison with other maps to provide researchers with efficient, intuitive tools to improve the understanding of their results. Each dataset and map is assigned a permanent Universal Resource Locator (URL), and all of the data is accessible through a REST Application Programming Interface (API). Additionally, the repository supports the NIDM-Results standard and has the ability to parse outputs from popular FSL and SPM software packages to automatically extract relevant metadata. This ease of use, modern web-integration, and pioneering functionality holds promise to improve the workflow for making inferences about and sharing whole-brain statistical maps. PMID:25869863

  16. NeuroVault.org: A repository for sharing unthresholded statistical maps, parcellations, and atlases of the human brain

    PubMed Central

    Gorgolewski, Krzysztof J.; Varoquaux, Gael; Rivera, Gabriel; Schwartz, Yannick; Sochat, Vanessa V.; Ghosh, Satrajit S.; Maumet, Camille; Nichols, Thomas E.; Poline, Jean-Baptiste; Yarkoni, Tal; Margulies, Daniel S.; Poldrack, Russell A.

    2016-01-01

    NeuroVault.org is dedicated to storing outputs of analyses in the form of statistical maps, parcellations and atlases, a unique strategy that contrasts with most neuroimaging repositories that store raw acquisition data or stereotaxic coordinates. Such maps are indispensable for performing meta-analyses, validating novel methodology, and deciding on precise outlines for regions of interest (ROIs). NeuroVault is open to maps derived from both healthy and clinical populations, as well as from various imaging modalities (sMRI, fMRI, EEG, MEG, PET, etc.). The repository uses modern web technologies such as interactive web-based visualization, cognitive decoding, and comparison with other maps to provide researchers with efficient, intuitive tools to improve the understanding of their results. Each dataset and map is assigned a permanent Universal Resource Locator (URL), and all of the data is accessible through a REST Application Programming Interface (API). Additionally, the repository supports the NIDM-Results standard, and has the ability to parse outputs from popular FSL and SPM software packages to automatically extract relevant metadata. This ease of use, modern web-integration, and pioneering functionality holds promise to improve the workflow for making inferences about and sharing whole-brain statistical maps. PMID:25869863

  17. Astronaut Allen during extravehicular activity (EVA) training in CCT

    NASA Technical Reports Server (NTRS)

    1993-01-01

    In the JSC Space Vehicle Mockup Facility, astronaut Andrew M. Allen retrieves gear to rehearse a suit-donning exercise on the middeck. Allen's very realistic environs are provided by the shuttle crew compartment trainer (CCT).

  18. Atlas of transgenic Tet-Off Ca2+/calmodulin-dependent protein kinase II and prion protein promoter activity in the mouse brain.

    PubMed

    Odeh, Francis; Leergaard, Trygve B; Boy, Jana; Schmidt, Thorsten; Riess, Olaf; Bjaalie, Jan G

    2011-02-14

    Conditional transgenic mouse models are important tools for investigations of neurodegenerative diseases and evaluation of potential therapeutic interventions. A popular conditional transgenic system is the binary tetracycline-responsive gene (Tet-Off) system, in which the expression of the gene of interest depends on a tetracycline-regulatable transactivator (tTA) under the control of a specific promoter construct. The most frequently used Tet-Off promoter mouse lines are the Ca(2+)/calmodulin-dependent protein kinase II (CamKII) and prion protein (PrP) promoter lines, respectively. To target the regulated gene of interest to relevant brain regions, a priori knowledge about the spatial distribution of the regulated gene expression in the brain is important. Such distribution patterns can be investigated using double transgenic mice in which the promoter construct regulates a LacZ reporter gene encoding the marker β-galactosidase which can be histologically detected using its substrate X-gal. We have previously published an atlas showing the brain-wide expression mediated by the Tet-Off PrP promoter mouse line, but the distribution of activity in the Tet-Off CamKII promoter mouse line is less well known. To compare promoter activity distributions in these two Tet-Off mouse lines, we have developed an online digital atlas tailored for side-by-side comparison of histological section images. The atlas provides a comprehensive list of brain regions containing X-gal labeling and an interactive dual image viewer tool for panning and zooming of corresponding section images. Comparison of spatial expression patterns between the two lines show considerable regional and cellular differences, relevant in context of generation and analysis of inducible models based on these two tetracycline responsive promoter mouse lines. PMID:21093594

  19. Brain in situ hybridization maps as a source for reverse-engineering transcriptional regulatory networks: Alzheimer's disease insights.

    PubMed

    Acquaah-Mensah, George K; Taylor, Ronald C

    2016-07-15

    Microarray data have been a valuable resource for identifying transcriptional regulatory relationships among genes. As an example, brain region-specific transcriptional regulatory events have the potential of providing etiological insights into Alzheimer Disease (AD). However, there is often a paucity of suitable brain-region specific expression data obtained via microarrays or other high throughput means. The Allen Brain Atlas in situ hybridization (ISH) data sets (Jones et al., 2009) represent a potentially valuable alternative source of high-throughput brain region-specific gene expression data for such purposes. In this study, Allen Brain Atlas mouse ISH data in the hippocampal fields were extracted, focusing on 508 genes relevant to neurodegeneration. Transcriptional regulatory networks were learned using three high-performing network inference algorithms. Only 17% of regulatory edges from a network reverse-engineered based on brain region-specific ISH data were also found in a network constructed upon gene expression correlations in mouse whole brain microarrays, thus showing the specificity of gene expression within brain sub-regions. Furthermore, the ISH data-based networks were used to identify instructive transcriptional regulatory relationships. Ncor2, Sp3 and Usf2 form a unique three-party regulatory motif, potentially affecting memory formation pathways. Nfe2l1, Egr1 and Usf2 emerge among regulators of genes involved in AD (e.g. Dhcr24, Aplp2, Tia1, Pdrx1, Vdac1, and Syn2). Further, Nfe2l1, Egr1 and Usf2 are sensitive to dietary factors and could be among links between dietary influences and genes in the AD etiology. Thus, this approach of harnessing brain region-specific ISH data represents a rare opportunity for gleaning unique etiological insights for diseases such as AD. PMID:27050105

  20. Rejuvenating Allen's Arc with the Geometric Mean.

    ERIC Educational Resources Information Center

    Phillips, William A.

    1994-01-01

    Contends that, despite ongoing criticism, Allen's arc elasticity formula remains entrenched in the microeconomics principles curriculum. Reviews the evolution and continuing scrutiny of the formula. Argues that the use of the geometric mean offers pedagogical advantages over the traditional arithmetic mean approach. (CFR)

  1. A chemical proteomic atlas of brain serine hydrolases identifies cell type-specific pathways regulating neuroinflammation

    PubMed Central

    Viader, Andreu; Ogasawara, Daisuke; Joslyn, Christopher M; Sanchez-Alavez, Manuel; Mori, Simone; Nguyen, William; Conti, Bruno; Cravatt, Benjamin F

    2016-01-01

    Metabolic specialization among major brain cell types is central to nervous system function and determined in large part by the cellular distribution of enzymes. Serine hydrolases are a diverse enzyme class that plays fundamental roles in CNS metabolism and signaling. Here, we perform an activity-based proteomic analysis of primary mouse neurons, astrocytes, and microglia to furnish a global portrait of the cellular anatomy of serine hydrolases in the brain. We uncover compelling evidence for the cellular compartmentalization of key chemical transmission pathways, including the functional segregation of endocannabinoid (eCB) biosynthetic enzymes diacylglycerol lipase-alpha (DAGLα) and –beta (DAGLβ) to neurons and microglia, respectively. Disruption of DAGLβ perturbed eCB-eicosanoid crosstalk specifically in microglia and suppressed neuroinflammatory events in vivo independently of broader effects on eCB content. Mapping the cellular distribution of metabolic enzymes thus identifies pathways for regulating specialized inflammatory responses in the brain while avoiding global alterations in CNS function. DOI: http://dx.doi.org/10.7554/eLife.12345.001 PMID:26779719

  2. ATLAS-1 Video News Release

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Allen Kenitzer, from Marshall Space Flight Center (MSFC), narrates this NASA Kennedy Space Center video presenting a MSFC-Television news release describing the overall scientific objectives of the Atmospheric Laboratory for Applications in Science-1 (ATLAS-1) Spacelab mission. Byron Lichtenberg (NASA Science Astronaut) and Anthony O'Neil (ATLAS-1 Mission Manager) explain that the 13 sophisticated and complementary instruments carried in shuttle Atlantis' payload bay are designed to identify the chemical species in our atmosphere, to measure the Sun's energy falling on and entering the atmosphere, to study the behavior of charged particles in the electric and magnetic fields surrounding the earth, and to gather ultraviolet light from stars and galaxies. ATLAS-1 is the first Spacelab flight of the National Aeronautics and Space Administration's (NASA's) Mission to Planet Earth.

  3. Subcortical physiology deformed into a patient-specific brain atlas for image-guided stereotaxy

    NASA Astrophysics Data System (ADS)

    Finnis, Kirk; Starreveld, Yves P.; Parrent, Andrew; Peters, Terence M.

    2002-05-01

    Stereotactic neurosurgery for movement disorders involves the accurate localization of functionally distinct subcortical anatomy that appears homogeneous on magnetic resonance or computed tomographic images. To aid localization of these surgical targets on patient images, we have developed a visualization oriented searchable and expandable database of functional organization representing bilaterally the sensorimotor thalamus, pallidum, internal capsule, and subthalamic nucleus. Data were obtained through microelectrode recording and stimulation mapping routinely performed during 123 functional stereotactic procedures. Electrophysiologic data were standardized using a multi-parameter coding system and annotated to their respective MRIs at the appropriate position in patient stereotactic space. To accommodate for normal anatomical variability, we have developed an intensity-based nonlinear registration algorithm that rapidly warps a patient's volumetric MRI to a high-resolution MRI average brain. The annotated functional data are subsequently transformed into the average brain coordinate system using the displacement grids generated by the algorithm. When the database is searched, clustering of like inter-patient physiologic responses within target anatomy and adjacent structures is revealed. These data may in turn be registered to a preoperative MRI using a desktop computer enabling prior to surgery interactive delineation of surgical targets. The database is expandable, fully searchable, and provides a visual 3D representation of subcortical functional organization.

  4. H. Julian Allen with Blunt Body Theory

    NASA Technical Reports Server (NTRS)

    1957-01-01

    H. Julian Allen is best known for his 'Blunt Body Theory' of aerodynamics, a design technique for alleviating the severe re-entry heating problem which was then delaying the development of ballistic missiles. His findings revolutionized the fundamental design of ballistic missle re-entry shapes. Subsequently, applied research led to applications of the 'blunt' shape to ballistic missles and spacecraft which were intended to re-enter the Earth's atmosphere. This application led to the design of ablative heat shields that protected the Mercury, Gemini and Apollo astronauts as their space capsules re- entered the Earth's atmosphere. 'Harvey' Allen as he was called by most, was not only a brilliant scientist and aeronautical engineer but was also admired for his kindness, thoughtfulness and sense of humor. Among his many other accomplishments, Harvey Allen served as Center Director of the NASA Ames Research Center from 1965 to 1969. He died of a heart attack on January 29, 1977 at the age of 66.

  5. An integrative analysis of regional gene expression profiles in the human brain.

    PubMed

    Myers, Emma M; Bartlett, Christopher W; Machiraju, Raghu; Bohland, Jason W

    2015-02-01

    Studies of the brain's transcriptome have become prominent in recent years, resulting in an accumulation of datasets with somewhat distinct attributes. These datasets, which are often analyzed only in isolation, also are often collected with divergent goals, which are reflected in their sampling properties. While many researchers have been interested in sampling gene expression in one or a few brain areas in a large number of subjects, recent efforts from the Allen Institute for Brain Sciences and others have focused instead on dense neuroanatomical sampling, necessarily limiting the number of individual donor brains studied. The purpose of the present work is to develop methods that draw on the complementary strengths of these two types of datasets for study of the human brain, and to characterize the anatomical specificity of gene expression profiles and gene co-expression networks derived from human brains using different specific technologies. The approach is applied using two publicly accessible datasets: (1) the high anatomical resolution Allen Human Brain Atlas (AHBA, Hawrylycz et al., 2012) and (2) a relatively large sample size, but comparatively coarse neuroanatomical dataset described previously by Gibbs et al. (2010). We found a relatively high degree of correspondence in differentially expressed genes and regional gene expression profiles across the two datasets. Gene co-expression networks defined in individual brain regions were less congruent, but also showed modest anatomical specificity. Using gene modules derived from the Gibbs dataset and from curated gene lists, we demonstrated varying degrees of anatomical specificity based on two classes of methods, one focused on network modularity and the other focused on enrichment of expression levels. Two approaches to assessing the statistical significance of a gene set's modularity in a given brain region were studied, which provide complementary information about the anatomical specificity of a gene

  6. A transcriptomic atlas of mouse neocortical layers.

    PubMed

    Belgard, T Grant; Marques, Ana C; Oliver, Peter L; Abaan, Hatice Ozel; Sirey, Tamara M; Hoerder-Suabedissen, Anna; García-Moreno, Fernando; Molnár, Zoltán; Margulies, Elliott H; Ponting, Chris P

    2011-08-25

    In the mammalian cortex, neurons and glia form a patterned structure across six layers whose complex cytoarchitectonic arrangement is likely to contribute to cognition. We sequenced transcriptomes from layers 1-6b of different areas (primary and secondary) of the adult (postnatal day 56) mouse somatosensory cortex to understand the transcriptional levels and functional repertoires of coding and noncoding loci for cells constituting these layers. A total of 5,835 protein-coding genes and 66 noncoding RNA loci are differentially expressed ("patterned") across the layers, on the basis of a machine-learning model (naive Bayes) approach. Layers 2-6b are each associated with specific functional and disease annotations that provide insights into their biological roles. This new resource (http://genserv.anat.ox.ac.uk/layers) greatly extends currently available resources, such as the Allen Mouse Brain Atlas and microarray data sets, by providing quantitative expression levels, by being genome-wide, by including novel loci, and by identifying candidate alternatively spliced transcripts that are differentially expressed across layers. PMID:21867878

  7. Three-dimensional brain atlas of pygmy squid, Idiosepius paradoxus, revealing the largest relative vertical lobe system volume among the cephalopods.

    PubMed

    Koizumi, Motoki; Shigeno, Shuichi; Mizunami, Makoto; Tanaka, Nobuaki K

    2016-07-01

    Cephalopods have the largest and most complex nervous system of all invertebrates, and the brain-to-body weight ratio exceeds those of most fish and reptiles. The brain is composed of lobe units, the functions of which have been studied through surgical manipulation and electrical stimulation. However, how information is processed in each lobe for the animal to make a behavioral decision has rarely been investigated. To perform such functional analyses, it is necessary to precisely describe how brain lobes are spatially organized and mutually interconnected as a whole. We thus made three-dimensional digital brain atlases of both hatchling and juvenile pygmy squid, Idiosepius paradoxus. I. paradoxus is the smallest squid and has a brain small enough to scan as a whole region in the field-of-view of a low-magnification laser scan microscope objective. Precise analyses of the confocal images of the brains revealed one newly identified lobe and also that the relative volume of the vertical lobe system, the higher association center, in the pygmy squid represents the largest portion compared with the cephalopod species reported previously. In addition, principal component analyses of relative volumes of lobe complexes revealed that the organization of I. paradoxus brain is comparable to those of Decapodiformes species commonly used to analyze complex behaviors such as Sepia officinalis and Sepioteuthis sepioidea. These results suggest that the pygmy squid can be a good model to investigate the brain functions of coleoids utilizing physiological methods. J. Comp. Neurol. 524:2142-2157, 2016. © 2016 Wiley Periodicals, Inc. PMID:26663197

  8. Atlas based brain volumetry: How to distinguish regional volume changes due to biological or physiological effects from inherent noise of the methodology.

    PubMed

    Opfer, Roland; Suppa, Per; Kepp, Timo; Spies, Lothar; Schippling, Sven; Huppertz, Hans-Jürgen

    2016-05-01

    Fully-automated regional brain volumetry based on structural magnetic resonance imaging (MRI) plays an important role in quantitative neuroimaging. In clinical trials as well as in clinical routine multiple MRIs of individual patients at different time points need to be assessed longitudinally. Measures of inter- and intrascanner variability are crucial to understand the intrinsic variability of the method and to distinguish volume changes due to biological or physiological effects from inherent noise of the methodology. To measure regional brain volumes an atlas based volumetry (ABV) approach was deployed using a highly elastic registration framework and an anatomical atlas in a well-defined template space. We assessed inter- and intrascanner variability of the method in 51 cognitively normal subjects and 27 Alzheimer dementia (AD) patients from the Alzheimer's Disease Neuroimaging Initiative by studying volumetric results of repeated scans for 17 compartments and brain regions. Median percentage volume differences of scan-rescans from the same scanner ranged from 0.24% (whole brain parenchyma in healthy subjects) to 1.73% (occipital lobe white matter in AD), with generally higher differences in AD patients as compared to normal subjects (e.g., 1.01% vs. 0.78% for the hippocampus). Minimum percentage volume differences detectable with an error probability of 5% were in the one-digit percentage range for almost all structures investigated, with most of them being below 5%. Intrascanner variability was independent of magnetic field strength. The median interscanner variability was up to ten times higher than the intrascanner variability. PMID:26723849

  9. High-resolution prediction of mouse brain connectivity using gene expression patterns.

    PubMed

    Fakhry, Ahmed; Ji, Shuiwang

    2015-02-01

    The brain is a multi-level system in which the high-level functions are generated by low-level genetic mechanisms. Thus, elucidating the relationship among multiple brain levels via correlative and predictive analytics is an important area in brain research. Currently, studies in multiple species have indicated that the spatiotemporal gene expression patterns are predictive of brain wiring. Specifically, results on the worm Caenorhabditis elegans have shown that the prediction of neuronal connectivity using gene expression signatures yielded statistically significant results. Recent studies on the mammalian brain produced similar results at the coarse regional level. In this study, we provide the first high-resolution, large-scale integrative analysis of the transcriptome and connectome in a single mammalian brain at a fine voxel level. By using the Allen Brain Atlas data, we predict voxel-level brain connectivity based on the gene expressions in the adult mouse brain. We employ regularized models to show that gene expression is predictive of connectivity at the voxel-level with an accuracy of 93%. We also identify a set of genes playing the most important role in connectivity prediction. We use only this small number of genes to predict the brain wiring with an accuracy over 80%. We discover that these important genes are enriched in neurons as compared to glia, and they perform connectivity-related functions. We perform several interesting correlative studies to further elucidate the transcriptome-connectome relationship. PMID:25109429

  10. Global differential expression of genes located in the Down Syndrome Critical Region in normal human brain

    PubMed Central

    Montoya, Julio Cesar; Fajardo, Dianora; Peña, Angela; Sánchez, Adalberto; Domínguez, Martha C; Satizábal, José María

    2014-01-01

    Background: The information of gene expression obtained from databases, have made possible the extraction and analysis of data related with several molecular processes involving not only in brain homeostasis but its disruption in some neuropathologies; principally in Down syndrome and the Alzheimer disease. Objective: To correlate the levels of transcription of 19 genes located in the Down Syndrome Critical Region (DSCR) with their expression in several substructures of normal human brain. Methods: There were obtained expression profiles of 19 DSCR genes in 42 brain substructures, from gene expression values available at the database of the human brain of the Brain Atlas of the Allen Institute for Brain Sciences", (http://human.brain-map.org/). The co-expression patterns of DSCR genes in brain were calculated by using multivariate statistical methods. Results: Highest levels of gene expression were registered at caudate nucleus, nucleus accumbens and putamen among central areas of cerebral cortex. Increased expression levels of RCAN1 that encode by a protein involved in signal transduction process of the CNS were recorded for PCP4 that participates in the binding to calmodulin and TTC3; a protein that is associated with differentiation of neurons. That previously identified brain structures play a crucial role in the learning process, in different class of memory and in motor skills. Conclusion: The precise regulation of DSCR gene expression is crucial to maintain the brain homeostasis, especially in those areas with high levels of gene expression associated with a remarkable process of learning and cognition. PMID:25767303

  11. Automated anatomical interpretation of ion distributions in tissue: linking imaging mass spectrometry to curated atlases.

    PubMed

    Verbeeck, Nico; Yang, Junhai; De Moor, Bart; Caprioli, Richard M; Waelkens, Etienne; Van de Plas, Raf

    2014-09-16

    Imaging mass spectrometry (IMS) has become a prime tool for studying the distribution of biomolecules in tissue. Although IMS data sets can become very large, computational methods have made it practically feasible to search these experiments for relevant findings. However, these methods lack access to an important source of information that many human interpretations rely upon: anatomical insight. In this work, we address this need by (1) integrating a curated anatomical data source with an empirically acquired IMS data source, establishing an algorithm-accessible link between them and (2) demonstrating the potential of such an IMS-anatomical atlas link by applying it toward automated anatomical interpretation of ion distributions in tissue. The concept is demonstrated in mouse brain tissue, using the Allen Mouse Brain Atlas as the curated anatomical data source that is linked to MALDI-based IMS experiments. We first develop a method to spatially map the anatomical atlas to the IMS data sets using nonrigid registration techniques. Once a mapping is established, a second computational method, called correlation-based querying, gives an elementary demonstration of the link by delivering basic insight into relationships between ion images and anatomical structures. Finally, a third algorithm moves further beyond both registration and correlation by providing automated anatomical interpretation of ion images. This task is approached as an optimization problem that deconstructs ion distributions as combinations of known anatomical structures. We demonstrate that establishing a link between an IMS experiment and an anatomical atlas enables automated anatomical annotation, which can serve as an important accelerator both for human and machine-guided exploration of IMS experiments. PMID:25153352

  12. Maximal tractable subclasses of Allen`s interval algebra: Preliminary report

    SciTech Connect

    Drakengren, T.; Jonsson, P.

    1996-12-31

    This paper continues Nebel and Burckert`s investigation of Allen`s interval algebra by presenting nine more maximal tractable subclasses of the algebra (provided that P {ne} NP), in addition to their previously reported ORD-Horn subclass. Furthermore, twelve tractable subclasses are identified, whose maximality is riot decided. Four of these can express the notion of sequentiality between intervals, which is not possible in the ORD-Horn algebra. The satisfiability algorithm, which is common for all the algebras, is shown to be linear.

  13. 4. Historic American Buildings Survey Harold Allen, Photographer 19 June ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. Historic American Buildings Survey Harold Allen, Photographer 19 June 1965 SANCTUARY FROM ENTRANCE - Holy Trinity Russian & Greek Orthodox Church, 1121 North Leavitt Street, Chicago, Cook County, IL

  14. 5. Historic American Buildings Survey Harold Allen, Photographer 19 June ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. Historic American Buildings Survey Harold Allen, Photographer 19 June 1965 ICONOSTASIS AND CHANDELIER - Holy Trinity Russian & Greek Orthodox Church, 1121 North Leavitt Street, Chicago, Cook County, IL

  15. Minerva Allen, "A Few Good Words": Interview with Minerva Allen, October 25, 1985.

    ERIC Educational Resources Information Center

    Scholer, Bo

    1987-01-01

    Minerva Allen, Assinibone tribal historian and mediator in dealings with off-reservation entities, talks about her poetry, prose, and songs; and her efforts to secure the continuance of tribal languages and traditions. Her role as an educator and writer of textbooks is also discussed. Selected poetry is included. (JMM)

  16. Expression Profiling of the Solute Carrier Gene Family in the Mouse BrainS⃞

    PubMed Central

    Dahlin, Amber; Royall, Josh; Hohmann, John G.; Wang, Joanne

    2009-01-01

    The solute carrier (Slc) superfamily is a major group of membrane transport proteins present in mammalian cells. Although Slc transporters play essential and diverse roles in the central nervous system, the localization and function of the vast majority of Slc genes in the mammalian brain are largely unknown. Using high-throughput in situ hybridization data generated by the Allen Brain Atlas, we systematically and quantitatively analyzed the spatial and cellular distribution of 307 Slc genes, which represent nearly 90% of presently known mouse Slc genes, in the adult C57BL/6J mouse brain. Our analysis showed that 252 (82%) of the 307 Slc genes are present in the brain, and a large proportion of these genes were detected at low to moderate expression levels. Evaluation of 20 anatomical brain subdivisions demonstrated a comparable level of Slc gene complexity but significant difference in transcript enrichment. The distribution of the expressed Slc genes was diverse, ranging from near-ubiquitous to highly localized. Functional annotation in 20 brain regions, including the blood-brain and blood-cerebral spinal fluid (CSF) barriers, suggests major roles of Slc transporters in supporting brain energy utilization, neurotransmission, nutrient supply, and CSF production. Furthermore, hierarchical cluster analysis revealed intricate Slc expression patterns associated with neuroanatomical organization. Our studies also revealed Slc genes present within defined brain microstructures and described the putative cell types expressing individual Slc genes. These results provide a useful resource for investigators to explore the roles of Slc genes in neurophysiological and pathological processes. PMID:19179540

  17. Brain-Derived Neurotrophic Factor and Antidepressive Effect of Electroconvulsive Therapy: Systematic Review and Meta-Analyses of the Preclinical and Clinical Literature

    PubMed Central

    Polyakova, M.; Schroeter, M. L.; Elzinga, B. M.; Holiga, S.; Schoenknecht, P.; de Kloet, E. R.; Molendijk, M. L.

    2015-01-01

    Emerging data suggest that Electro-Convulsive Treatment (ECT) may reduce depressive symptoms by increasing the expression of Brain-Derived Neurotrophic Factor (BDNF). Yet, conflicting findings have been reported. For this reason we performed a systematic review and meta-analysis of the preclinical and clinical literature on the association between ECT treatment (ECS in animals) and changes in BDNF concentrations and their effect on behavior. In addition, regional brain expression of BDNF in mouse and human brains were compared using Allen Brain Atlas. ECS, over sham, increased BDNF mRNA and protein in animal brain (effect size [Hedge’s g]: 0.38―0.54; 258 effect-size estimates, N = 4,284) but not in serum (g = 0.06, 95% CI = -0.05―0.17). In humans, plasma but not serum BDNF increased following ECT (g = 0.72 vs. g = 0.14; 23 effect sizes, n = 281). The gradient of the BDNF increment in animal brains corresponded to the gradient of the BDNF gene expression according to the Allen brain atlas. Effect-size estimates were larger following more ECT sessions in animals (r = 0.37, P < .0001) and in humans (r = 0.55; P = 0.05). There were some indications that the increase in BDNF expression was associated with behavioral changes in rodents, but not in humans. We conclude that ECS in rodents and ECT in humans increase BDNF concentrations but this is not consistently associated with changes in behavior. PMID:26529101

  18. SETI Surveys on the Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Backus, Peter R.; Kilsdonk, T. N.; ATA Team

    2009-01-01

    The Allen Telescope Array (ATA-42) is a centimeter-wave array of 42 six-meter dishes that allows simultaneous SETI and other radio astronomy projects. In this paper we report on initial SETI observations using several observation and RFI mitigation strategies. We conducted both "targeted” observations of selected stars and "sky survey” observations of areas of the sky. Some observations were done with the SETI project directing the pointing of the array and others were "commensal,” in a direction selected by another project. In both modes, SETI observations used an independent RF tuning and two synthesized beams pointing at stars or positions in the field of view and tuned to the same frequency band. Results of the two SETI observations were compared and used to excise interference. In some observations, each beam had a null positioned at the center of the other beam. In the long term, we plan to observe one million target stars and survey large sections of the galactic plane over the frequency range from 1 GHz to 10 GHz. Much of this work may be done in parallel with other large-scale surveys. The first phase of the ATA was funded through generous grants from the Paul G. Allen Family Foundation. UC Berkeley, the SETI Institute, the National Science Foundation (Grant No. 0540599), Sun Microsystems, Xilinx, Nathan Myhrvold, Greg Papadopoulos, and other corporations and individual donors contributed additional funding.

  19. Brain

    MedlinePlus

    ... will return after updating. Resources Archived Modules Updates Brain Cerebrum The cerebrum is the part of the ... the outside of the brain and spinal cord. Brain Stem The brain stem is the part of ...

  20. Individual 3D region-of-interest atlas of the human brain: neural-network-based tissue classification with automatic training point extraction

    NASA Astrophysics Data System (ADS)

    Wagenknecht, Gudrun; Kaiser, Hans-Juergen; Obladen, Thorsten; Sabri, Osama; Buell, Udalrich

    2000-06-01

    The purpose of individual 3D region-of-interest atlas extraction is to automatically define anatomically meaningful regions in 3D MRI images for quantification of functional parameters (PET, SPECT: rMRGlu, rCBF). The first step of atlas extraction is to automatically classify brain tissue types into gray matter (GM), white matter (WM), cerebrospinal fluid (CSF), scalp/bone (SB) and background (BG). A feed-forward neural network with back-propagation training algorithm is used and compared to other numerical classifiers. It can be trained by a sample from the individual patient data set in question. Classification is done by a 'winner takes all' decision. Automatic extraction of a user-specified number of training points is done in a cross-sectional slice. Background separation is done by simple region growing. The most homogeneous voxels define the region for WM training point extraction (TPE). Non-white-matter and nonbackground regions are analyzed for GM and CSF training points. For SB TPE, the distance from the BG region is one feature. For each class, spatially uniformly distributed training points are extracted by a random generator from these regions. Simulated and real 3D MRI images are analyzed and error rates for TPE and classification calculated. The resulting class images can be analyzed for extraction of anatomical ROIs.

  1. Sensitivity analysis and automation for intraoperative implementation of the atlas-based method for brain shift correction

    NASA Astrophysics Data System (ADS)

    Chen, Ishita; Simpson, Amber L.; Sun, Kay; Thompson, Reid C.; Miga, Michael I.

    2013-03-01

    The use of biomechanical models to correct the misregistration due to deformation in image guided neurosurgical systems has been a growing area of investigation. In previous work, an atlas-based inverse model was developed to account for soft-tissue deformations during image-guided surgery. Central to that methodology is a considerable amount of pre-computation and planning. The goal of this work is to evaluate techniques that could potentially reduce that burden. Distinct from previous manual techniques, an automated segmentation technique is described for the cerebrum and dural septa. The shift correction results using this automated segmentation method were compared to those using the manual methods. In addition, the extent and distribution of the surgical parameters associated with the deformation atlas were investigated by a sensitivity analysis using simulation experiments and clinical data. The shift correction results did not change significantly using the automated method (correction of 73+/-13% ) as compared to the semi-automated method from previous work (correction of 76+/-13%). The results of the sensitivity analysis show that the atlas could be constructed by coarser sampling (six fold reduction) without substantial degradation in the shift reconstruction, a decrease in preoperative computational time from 13.1+/-3.5 hours to 2.2+/-0.6 hours. The automated segmentation technique and the findings of the sensitivity study have significant impact on the reduction of pre-operative computational time, improving the utility of the atlas-based method. The work in this paper suggests that the atlas-based technique can become a `time of surgery' setup procedure rather than a pre-operative computing strategy.

  2. Mission Specialist (MS) Allen experiments with beverage on middeck

    NASA Technical Reports Server (NTRS)

    1982-01-01

    Mission Specialist (MS) Allen, using beverage container and drinking straw, experiments with microgravity chararcteristics of orange juice on middeck in front of the Development Flight Instrument (DFI) unit and forward lockers. Allen laughes as he watches the results of his experimentation.

  3. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  4. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  5. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  6. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  7. 33 CFR 80.1440 - Port Allen, Kauai, HI.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Port Allen, Kauai, HI. 80.1440 Section 80.1440 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1440 Port Allen, Kauai, HI. A line drawn...

  8. Human brain atlas for automated region of interest selection in quantitative susceptibility mapping: application to determine iron content in deep gray matter structures

    PubMed Central

    Lim, Issel Anne L.; Faria, Andreia V.; Li, Xu; Hsu, Johnny T.C.; Airan, Raag D.; Mori, Susumu; van Zijl, Peter C. M.

    2013-01-01

    The purpose of this paper is to extend the single-subject Eve atlas from Johns Hopkins University, which currently contains diffusion tensor and T1-weighted anatomical maps, by including contrast based on quantitative susceptibility mapping. The new atlas combines a “deep gray matter parcellation map” (DGMPM) derived from a single-subject quantitative susceptibility map with the previously established “white matter parcellation map” (WMPM) from the same subject’s T1-weighted and diffusion tensor imaging data into an MNI coordinate map named the “Everything Parcellation Map in Eve Space,” also known as the “EvePM.” It allows automated segmentation of gray matter and white matter structures. Quantitative susceptibility maps from five healthy male volunteers (30 to 33 years of age) were coregistered to the Eve Atlas with AIR and Large Deformation Diffeomorphic Metric Mapping (LDDMM), and the transformation matrices were applied to the EvePM to produce automated parcellation in subject space. Parcellation accuracy was measured with a kappa analysis for the left and right structures of six deep gray matter regions. For multi-orientation QSM images, the Kappa statistic was 0.85 between automated and manual segmentation, with the inter-rater reproducibility Kappa being 0.89 for the human raters, suggesting “almost perfect” agreement between all segmentation methods. Segmentation seemed slightly more difficult for human raters on single-orientation QSM images, with the Kappa statistic being 0.88 between automated and manual segmentation, and 0.85 and 0.86 between human raters. Overall, this atlas provides a time-efficient tool for automated coregistration and segmentation of quantitative susceptibility data to analyze many regions of interest. These data were used to establish a baseline for normal magnetic susceptibility measurements for over 60 brain structures of 30- to 33-year-old males. Correlating the average susceptibility with age-based iron

  9. Segmentation of brain magnetic resonance images based on multi-atlas likelihood fusion: testing using data with a broad range of anatomical and photometric profiles

    PubMed Central

    Tang, Xiaoying; Crocetti, Deana; Kutten, Kwame; Ceritoglu, Can; Albert, Marilyn S.; Mori, Susumu; Mostofsky, Stewart H.; Miller, Michael I.

    2015-01-01

    We propose a hierarchical pipeline for skull-stripping and segmentation of anatomical structures of interest from T1-weighted images of the human brain. The pipeline is constructed based on a two-level Bayesian parameter estimation algorithm called multi-atlas likelihood fusion (MALF). In MALF, estimation of the parameter of interest is performed via maximum a posteriori estimation using the expectation-maximization (EM) algorithm. The likelihoods of multiple atlases are fused in the E-step while the optimal estimator, a single maximizer of the fused likelihoods, is then obtained in the M-step. There are two stages in the proposed pipeline; first the input T1-weighted image is automatically skull-stripped via a fast MALF, then internal brain structures of interest are automatically extracted using a regular MALF. We assess the performance of each of the two modules in the pipeline based on two sets of images with markedly different anatomical and photometric contrasts; 3T MPRAGE scans of pediatric subjects with developmental disorders vs. 1.5T SPGR scans of elderly subjects with dementia. Evaluation is performed quantitatively using the Dice overlap as well as qualitatively via visual inspections. As a result, we demonstrate subject-level differences in the performance of the proposed pipeline, which may be accounted for by age, diagnosis, or the imaging parameters (particularly the field strength). For the subcortical and ventricular structures of the two datasets, the hierarchical pipeline is capable of producing automated segmentations with Dice overlaps ranging from 0.8 to 0.964 when compared with the gold standard. Comparisons with other representative segmentation algorithms are presented, relative to which the proposed hierarchical pipeline demonstrates comparative or superior accuracy. PMID:25784852

  10. Neonatal Atlas Construction Using Sparse Representation

    PubMed Central

    Shi, Feng; Wang, Li; Wu, Guorong; Li, Gang; Gilmore, John H.; Lin, Weili; Shen, Dinggang

    2014-01-01

    Atlas construction generally includes first an image registration step to normalize all images into a common space and then an atlas building step to fuse the information from all the aligned images. Although numerous atlas construction studies have been performed to improve the accuracy of the image registration step, unweighted or simply weighted average is often used in the atlas building step. In this article, we propose a novel patch-based sparse representation method for atlas construction after all images have been registered into the common space. By taking advantage of local sparse representation, more anatomical details can be recovered in the built atlas. To make the anatomical structures spatially smooth in the atlas, the anatomical feature constraints on group structure of representations and also the overlapping of neighboring patches are imposed to ensure the anatomical consistency between neighboring patches. The proposed method has been applied to 73 neonatal MR images with poor spatial resolution and low tissue contrast, for constructing a neonatal brain atlas with sharp anatomical details. Experimental results demonstrate that the proposed method can significantly enhance the quality of the constructed atlas by discovering more anatomical details especially in the highly convoluted cortical regions. The resulting atlas demonstrates superior performance of our atlas when applied to spatially normalizing three different neonatal datasets, compared with other start-of-the-art neonatal brain atlases. PMID:24638883

  11. Identification of a set of genes showing regionally enriched expression in the mouse brain

    PubMed Central

    D'Souza, Cletus A; Chopra, Vikramjit; Varhol, Richard; Xie, Yuan-Yun; Bohacec, Slavita; Zhao, Yongjun; Lee, Lisa LC; Bilenky, Mikhail; Portales-Casamar, Elodie; He, An; Wasserman, Wyeth W; Goldowitz, Daniel; Marra, Marco A; Holt, Robert A; Simpson, Elizabeth M; Jones, Steven JM

    2008-01-01

    Background The Pleiades Promoter Project aims to improve gene therapy by designing human mini-promoters (< 4 kb) that drive gene expression in specific brain regions or cell-types of therapeutic interest. Our goal was to first identify genes displaying regionally enriched expression in the mouse brain so that promoters designed from orthologous human genes can then be tested to drive reporter expression in a similar pattern in the mouse brain. Results We have utilized LongSAGE to identify regionally enriched transcripts in the adult mouse brain. As supplemental strategies, we also performed a meta-analysis of published literature and inspected the Allen Brain Atlas in situ hybridization data. From a set of approximately 30,000 mouse genes, 237 were identified as showing specific or enriched expression in 30 target regions of the mouse brain. GO term over-representation among these genes revealed co-involvement in various aspects of central nervous system development and physiology. Conclusion Using a multi-faceted expression validation approach, we have identified mouse genes whose human orthologs are good candidates for design of mini-promoters. These mouse genes represent molecular markers in several discrete brain regions/cell-types, which could potentially provide a mechanistic explanation of unique functions performed by each region. This set of markers may also serve as a resource for further studies of gene regulatory elements influencing brain expression. PMID:18625066

  12. Freeman Allen: Boston's pioneering physician anesthetist.

    PubMed

    Morris, Samuel D; Morris, Alina J; Rockoff, Mark A

    2014-11-01

    On October 16, 1846 dentist William T. G. Morton successfully demonstrated at the Massachusetts General Hospital that ether could prevent the pain of surgery. For decades afterwards, the administration of anesthesia in the United States was generally relegated to dentists, medical students, junior surgical trainees, or even nonmedical personnel. It was not until the end of the 19th century that a few pioneering physicians began devoting their careers to administering anesthesia to patients, studying ways to make it safer and more effective, and teaching others about its use. One of these individuals was Freeman Allen, who was appointed the first physician anesthetist to the medical staff at the Massachusetts General Hospital and several other major hospitals in Boston. We describe this remarkable man, his contributions to the early development of anesthesiology as a medical specialty, and the true cause of his untimely death. PMID:25329027

  13. Functional associations among G protein-coupled neurotransmitter receptors in the human brain

    PubMed Central

    2014-01-01

    Background The activity of neurons is controlled by groups of neurotransmitter receptors rather than by individual receptors. Experimental studies have investigated some receptor interactions, but currently little information is available about transcriptional associations among receptors at the whole-brain level. Results A total of 4950 correlations between 100 G protein-coupled neurotransmitter receptors were examined across 169 brain regions in the human brain using expression data published in the Allen Human Brain Atlas. A large number of highly significant correlations were found, many of which have not been investigated in hypothesis-driven studies. The highest positive and negative correlations of each receptor are reported, which can facilitate the construction of receptor sets likely to be affected by altered transcription of one receptor (such sets always exist, but their members are difficult to predict). A graph analysis isolated two large receptor communities, within each of which receptor mRNA levels were strongly cross-correlated. Conclusions The presented systematic analysis shows that the mRNA levels of many G protein-coupled receptors are interdependent. This finding is not unexpected, since the brain is a highly integrated complex system. However, the analysis also revealed two novel properties of global brain structure. First, receptor correlations are described by a simple statistical distribution, which suggests that receptor interactions may be guided by qualitatively similar processes. Second, receptors appear to form two large functional communities, which might be differentially affected in brain disorders. PMID:24438157

  14. A method based on Monte Carlo simulations and voxelized anatomical atlases to evaluate and correct uncertainties on radiotracer accumulation quantitation in beta microprobe studies in the rat brain

    NASA Astrophysics Data System (ADS)

    Pain, F.; Dhenain, M.; Gurden, H.; Routier, A. L.; Lefebvre, F.; Mastrippolito, R.; Lanièce, P.

    2008-10-01

    The β-microprobe is a simple and versatile technique complementary to small animal positron emission tomography (PET). It relies on local measurements of the concentration of positron-labeled molecules. So far, it has been successfully used in anesthetized rats for pharmacokinetics experiments and for the study of brain energetic metabolism. However, the ability of the technique to provide accurate quantitative measurements using 18F, 11C and 15O tracers is likely to suffer from the contribution of 511 keV gamma rays background to the signal and from the contribution of positrons from brain loci surrounding the locus of interest. The aim of the present paper is to provide a method of evaluating several parameters, which are supposed to affect the quantification of recordings performed in vivo with this methodology. We have developed realistic voxelized phantoms of the rat whole body and brain, and used them as input geometries for Monte Carlo simulations of previous β-microprobe reports. In the context of realistic experiments (binding of 11C-Raclopride to D2 dopaminergic receptors in the striatum; local glucose metabolic rate measurement with 18F-FDG and H2O15 blood flow measurements in the somatosensory cortex), we have calculated the detection efficiencies and corresponding contribution of 511 keV gammas from peripheral organs accumulation. We confirmed that the 511 keV gammas background does not impair quantification. To evaluate the contribution of positrons from adjacent structures, we have developed β-Assistant, a program based on a rat brain voxelized atlas and matrices of local detection efficiencies calculated by Monte Carlo simulations for several probe geometries. This program was used to calculate the 'apparent sensitivity' of the probe for each brain structure included in the detection volume. For a given localization of a probe within the brain, this allows us to quantify the different sources of beta signal. Finally, since stereotaxic accuracy is

  15. 12. Historic American Buildings Survey Allen L. Hubbard, Photographer December ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    12. Historic American Buildings Survey Allen L. Hubbard, Photographer December 1, 1936 CHEST (North room 3rd floor) (SWISS FURNITURE) - Fort Western, Main Building, Bowman Street, Augusta, Kennebec County, ME

  16. 13. Historic American Buildings Survey Allen L. Hubbard, Photographer December ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    13. Historic American Buildings Survey Allen L. Hubbard, Photographer December 1, 1936 CHEST (North room 3rd floor) (SWISS FURNITURE) - Fort Western, Main Building, Bowman Street, Augusta, Kennebec County, ME

  17. 9. Historic American Buildings Survey Harold Allen, Photographer June 1964 ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. Historic American Buildings Survey Harold Allen, Photographer June 1964 Gilded Relief Decoration, Detail of Frieze at Base of Chancel Arch - Kehilath Anshe Ma'ariv Synagogue, 3301 South Indiana Avenue, Chicago, Cook County, IL

  18. 8. Historic American Buildings Survey Harold Allen, Photographer June 1964 ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. Historic American Buildings Survey Harold Allen, Photographer June 1964 GILDED RELIEF DECORATION ON FACE OF CHANCEL ARCH - Kehilath Anshe Ma'ariv Synagogue, 3301 South Indiana Avenue, Chicago, Cook County, IL

  19. 4. Historic American Buildings Survey Harold Allen, Photographer June 1964 ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. Historic American Buildings Survey Harold Allen, Photographer June 1964 AUDITORIUM, FROM BALCONY-- LOOKING NORTHWEST - Kehilath Anshe Ma'ariv Synagogue, 3301 South Indiana Avenue, Chicago, Cook County, IL

  20. 3. Historic American Buildings Survey Harold Allen, Photographer June 1964 ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. Historic American Buildings Survey Harold Allen, Photographer June 1964 Auditorium, from Balcony, looking Northeast - Kehilath Anshe Ma'ariv Synagogue, 3301 South Indiana Avenue, Chicago, Cook County, IL

  1. 1. Historic American Buildings Survey Harold Allen, Photographer 31 May ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. Historic American Buildings Survey Harold Allen, Photographer 31 May 1964 WEST (NORMAL AVE.) AND SOUTHEAST (CANALPORT AVE.) ELEVATIONS - Schoenhofen Brewing Company, Powerhouse, 1770 Canalport Avenue, Chicago, Cook County, IL

  2. 3. Historic American Buildings Survey Harold Allen, Photographer 3 May ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. Historic American Buildings Survey Harold Allen, Photographer 3 May 1965 ENTRANCE CANOPY FROM SOUTHWEST - Holy Trinity Russian & Greek Orthodox Church, 1121 North Leavitt Street, Chicago, Cook County, IL

  3. Historic American Buildings Survey Harold Allen, Photographer, June, 1964 VIEW: ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Historic American Buildings Survey Harold Allen, Photographer, June, 1964 VIEW: EXTERIOR: WEST (CLARK STREET) AND SOUTH (JACKSON BLVD.) SIDES - U.S. Post Office, Customs House & Sub-Treasury, 218 South Dearborn Street, Chicago, Cook County, IL

  4. Historic American Buildings Survey Harold Allen, Photographer, June, 1964 VIEW: ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Historic American Buildings Survey Harold Allen, Photographer, June, 1964 VIEW: CENTRAL HALL, LOOKING ACROSS FROM THE SIXTH FLOOR - U.S. Post Office, Customs House & Sub-Treasury, 218 South Dearborn Street, Chicago, Cook County, IL

  5. Historic American Buildings Survey Harold Allen, Photographer, June, 1964 VIEW: ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Historic American Buildings Survey Harold Allen, Photographer, June, 1964 VIEW: CENTRAL HALL, FROM THE SIXTH FLOOR LOOKING NORTHWEST - U.S. Post Office, Customs House & Sub-Treasury, 218 South Dearborn Street, Chicago, Cook County, IL

  6. 2. Historic American Buildings Survey Harold Allen, Photographer 14 June ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. Historic American Buildings Survey Harold Allen, Photographer 14 June 1964 TOP THREE FLOORS, MIDDLE BAY, SOUTH (FRONT) ELEVATION - Chicago Criminal Courts Building, 54 West Hubbard Street, Chicago, Cook County, IL

  7. 8. Historic American Buildings Survey Harold Allen, Photographer 24 June ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. Historic American Buildings Survey Harold Allen, Photographer 24 June 1964 GRAND STAIRWAY, FROM SECOND FLOOR HALL, SHOWING STAINED GLASS WINDOW IN WEST WALL ABOVE LANDING - Francis J. Dewes House, 503 West Wrightwood Avenue, Chicago, Cook County, IL

  8. 6. Historic American Buildings Survey Harold Allen, Photographer June 1964 ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. Historic American Buildings Survey Harold Allen, Photographer June 1964 STAINED GLASS WINDOW, WEST WINDOW IN SOUTH WALL, FROM BALCONY - Kehilath Anshe Ma'ariv Synagogue, 3301 South Indiana Avenue, Chicago, Cook County, IL

  9. A Summing Up. Allen Memorial Art Museum Addition, Oberlin, Ohio

    ERIC Educational Resources Information Center

    Progressive Architecture, 1977

    1977-01-01

    Venturi and Rauch's addition to the Allen Art Museum at Oberlin College is in two separate parts: a loft that houses new facilities for the art department and a gallery for contemporary art. (Author/MLF)

  10. The conversion of allenes to strained three-membered heterocycles.

    PubMed

    Adams, C S; Weatherly, C D; Burke, E G; Schomaker, J M

    2014-05-01

    This article reviews methods for converting allenes to strained, three-membered methylene heterocycles, and also covers the reactivity of these products. Specifically, the synthesis and reactivity of methylene aziridines, allene oxides/spirodiepoxides, methylene silacyclopropanes, methylene phosphiranes, and methylene thiiranes are described, including applications to the synthesis of complex molecules. Due to the primary focus on heterocyclic motifs, the all-carbon analogue of these species (methylene cyclopropane) is only briefly discussed. PMID:24647416

  11. Chemoselective allene aziridination via Ag(I) catalysis.

    PubMed

    Rigoli, Jared W; Weatherly, Cale D; Vo, Brian T; Neale, Samuel; Meis, Alan R; Schomaker, Jennifer M

    2013-01-18

    Allene aziridination generates useful bicyclic methylene aziridine scaffolds that can be flexibly transformed into a range of stereochemically complex and densely functionalized amine-containing stereotriads. The scope of this chemistry has been limited by the poor chemoselectivity that often results when typical dinuclear Rh(II) catalysts are employed with homoallenic carbamates. Herein, Ag(I) catalysts that significantly improve the scope and yield of bicyclic methylene aziridines that can be prepared via allene aziridination are described. PMID:23265391

  12. Chemoselective Allene Aziridination via Ag(I) Catalysis

    PubMed Central

    Rigoli, Jared W.; Weatherly, Cale D.; Vo, Brian T.; Neale, Samuel; Meis, Alan R.

    2015-01-01

    Allene aziridination generates useful bicyclic methylene aziridine scaffolds that can be flexibly transformed into a range of stereochemically complex and densely functionalized amine-containing stereotriads. The scope of this chemistry has been limited by the poor chemoselectivity that often results when typical dinuclear Rh(II) catalysts are employed with homoallenic carbamates. Herein, Ag(I) catalysts that significantly improve the scope and yield of bicyclic methylene aziridines that can be prepared via allene aziridination are described. PMID:23265391

  13. Voices: A Conversation with Allen J. Wilcox.

    PubMed

    Jukic, Anne Marie Z

    2016-09-01

    Allen James Wilcox was born on 30 September 1946 in Columbus, OH. He studied medicine at the University of Michigan, graduated in 1973, and after a rotating internship, he completed a master's degree in maternal and child health (1976) and a PhD in epidemiology (1979) at the University of North Carolina in Chapel Hill. After graduation, he went to work at the National Institute of Environmental Health Sciences (NIEHS, one of the US National Institutes of Health) in Durham, NC, where he has spent his career. He developed a research program in reproductive and perinatal epidemiology, a relatively unexplored area at the time. His studies include the early pregnancy study, which documented the extent of subclinical pregnancy loss in humans and established the fertile days of a woman's menstrual cycle. He served as the Chief of the Epidemiology Branch from 1991 to 2001, and as Editor-in-Chief of the journal EPIDEMIOLOGY from 2001 to 2014. His textbook, Fertility and Pregnancy-An Epidemiologic Perspective, was published by Oxford University Press in 2010. He was elected to the American Epidemiological Society in 1989, and served as its president in 2003. He also served as president of the Society of Pediatric and Perinatal Epidemiological Research (1996) and the president of the Society of Epidemiological Research (1998). He holds adjunct teaching appointments at the University of North Carolina, Harvard University, and the University of Bergen (Norway), which awarded him an honorary doctoral degree in 2008. PMID:27482869

  14. Substituent effects on dynamics at conical intersections: Allene and methyl allenes

    NASA Astrophysics Data System (ADS)

    Neville, Simon P.; Wang, Yanmei; Boguslavskiy, Andrey E.; Stolow, Albert; Schuurman, Michael S.

    2016-01-01

    We report a joint experimental and theoretical study on the ultrafast excited state dynamics of allene and a series of its methylated analogues (1,2-butadiene, 1,1-dimethylallene, and tetramethylallene) in order to elucidate the conical intersection mediated dynamics that give rise to ultrafast relaxation to the ground electronic state. We use femtosecond time-resolved photoelectron spectroscopy (TRPES) to probe the coupled electronic-vibrational dynamics following UV excitation at 200 nm (6.2 eV). Ab initio multiple spawning (AIMS) simulations are employed to determine the mechanistic details of two competing dynamical pathways to the ground electronic state. In all molecules, these pathways are found to involve as follows: (i) twisting about the central allenic C-C-C axis followed by pyramidalization at one of the terminal carbon atoms and (ii) bending of allene moiety. Importantly, the AIMS trajectory data were used for ab initio simulations of the TRPES, permitting direct comparison with experiment. For each molecule, the decay of the TRPES signal is characterized by short (30 fs, 52 fs, 23 fs) and long (1.8 ps, 3.5 ps, [306 fs, 18 ps]) time constants for 1,2-butadiene, 1,1-dimethylallene, and tetramethylallene, respectively. However, AIMS simulations show that these time constants are only loosely related to the evolution of electronic character and actually more closely correlate to large amplitude motions on the electronic excited state, modulating the instantaneous vertical ionization potentials. Furthermore, the fully substituted tetramethylallene is observed to undergo qualitatively different dynamics, as displacements involving the relatively massive methyl groups impede direct access to the conical intersections which give rise to the ultrafast relaxation dynamics observed in the other species. These results show that the branching between the "twisting" and "bending" pathways can be modified via the selective methylation of the terminal carbon atoms of

  15. 33 CFR 165.T08-0432 - Safety Zone; Waterway Closure, Morgan City-Port Allen Route from Mile Marker 0 to Port Allen Lock.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., Morgan City-Port Allen Route from Mile Marker 0 to Port Allen Lock. 165.T08-0432 Section 165.T08-0432... Limited Access Areas Eighth Coast Guard District § 165.T08-0432 Safety Zone; Waterway Closure, Morgan City... Water Way on the Morgan City—Port Allen route from MM 0 to the Port Allen lock. (b) Effective date....

  16. Reactivity and Chemoselectivity of Allenes in Rh(I)-Catalyzed Intermolecular (5 + 2) Cycloadditions with Vinylcyclopropanes: Allene-Mediated Rhodacycle Formation Can Poison Rh(I)-Catalyzed Cycloadditions

    PubMed Central

    2015-01-01

    Allenes are important 2π building blocks in organic synthesis and engage as 2-carbon components in many metal-catalyzed reactions. Wender and co-workers discovered that methyl substituents on the terminal allene double bond counterintuitively change the reactivities of allenes in [Rh(CO)2Cl]2-catalyzed intermolecular (5 + 2) cycloadditions with vinylcyclopropanes (VCPs). More sterically encumbered allenes afford higher cycloadduct yields, and such effects are also observed in other Rh(I)-catalyzed intermolecular cycloadditions. Through density functional theory calculations (B3LYP and M06) and experiment, we explored this enigmatic reactivity and selectivity of allenes in [Rh(CO)2Cl]2-catalyzed intermolecular (5 + 2) cycloadditions with VCPs. The apparent low reactivity of terminally unsubstituted allenes is associated with a competing allene dimerization that irreversibly sequesters rhodium. With terminally substituted allenes, steric repulsion between the terminal substituents significantly increases the barrier of allene dimerization while the barrier of the (5 + 2) cycloaddition is not affected, and thus the cycloaddition prevails. Computation has also revealed the origin of chemoselectivity in (5 + 2) cycloadditions with allene-ynes. Although simple allene and acetylene have similar reaction barriers, intermolecular (5 + 2) cycloadditions of allene-ynes occur exclusively at the terminal allene double bond. The terminal double bond is more reactive due to the enhanced d−π* backdonation. At the same time, insertion of the internal double bond of an allene-yne has a higher barrier as it would break π conjugation. Substituted alkynes are more difficult to insert compared with acetylene, because of the steric repulsion from the additional substituents. This leads to the greater reactivity of the allene double bond relative to the alkynyl group in allene-ynes. PMID:25379606

  17. Common Genetic Variant in VIT Is Associated with Human Brain Asymmetry

    PubMed Central

    Tadayon, Sayed H.; Vaziri-Pashkam, Maryam; Kahali, Pegah; Ansari Dezfouli, Mitra; Abbassian, Abdolhossein

    2016-01-01

    Brain asymmetry varies across individuals. However, genetic factors contributing to this normal variation are largely unknown. Here we studied variation of cortical surface area asymmetry in a large sample of subjects. We performed principal component analysis (PCA) to capture correlated asymmetry variation across cortical regions. We found that caudal and rostral anterior cingulate together account for a substantial part of asymmetry variation among individuals. To find SNPs associated with this subset of brain asymmetry variation we performed a genome-wide association study followed by replication in an independent cohort. We identified one SNP (rs11691187) that had genome-wide significant association (PCombined = 2.40e-08). The rs11691187 is in the first intron of VIT. In a follow-up analysis, we found that VIT gene expression is associated with brain asymmetry in six donors of the Allen Human Brain Atlas. Based on these findings we suggest that VIT contributes to normal brain asymmetry variation. Our results can shed light on disorders associated with altered brain asymmetry. PMID:27252636

  18. Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain

    PubMed Central

    Chou, Shen-Ju; Wang, Chindi; Sintupisut, Nardnisa; Niou, Zhen-Xian; Lin, Chih-Hsu; Li, Ker-Chau; Yeang, Chen-Hsiang

    2016-01-01

    Allen Brain Atlas (ABA) provides a valuable resource of spatial/temporal gene expressions in mammalian brains. Despite rich information extracted from this database, current analyses suffer from several limitations. First, most studies are either gene-centric or region-centric, thus are inadequate to capture the superposition of multiple spatial-temporal patterns. Second, standard tools of expression analysis such as matrix factorization can capture those patterns but do not explicitly incorporate spatial dependency. To overcome those limitations, we proposed a computational method to detect recurrent patterns in the spatial-temporal gene expression data of developing mouse brains. We demonstrated that regional distinction in brain development could be revealed by localized gene expression patterns. The patterns expressed in the forebrain, medullary and pontomedullary, and basal ganglia are enriched with genes involved in forebrain development, locomotory behavior, and dopamine metabolism respectively. In addition, the timing of global gene expression patterns reflects the general trends of molecular events in mouse brain development. Furthermore, we validated functional implications of the inferred patterns by showing genes sharing similar spatial-temporal expression patterns with Lhx2 exhibited differential expression in the embryonic forebrains of Lhx2 mutant mice. These analysis outcomes confirm the utility of recurrent expression patterns in studying brain development. PMID:26786896

  19. 76 FR 36318 - Safety Zone; Waterway Closure, Morgan City-Port Allen Route From Mile Marker 0 to Port Allen Lock

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-22

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Waterway Closure, Morgan City-Port Allen..., design, or operation; test methods; sampling procedures; and related management systems practices) that...; Waterway Closure, Morgan City-Port Allen Route from Mile Marker 0 to Port Allen Lock. (a) Location....

  20. Biosynthesis of allene oxides in Physcomitrella patens

    PubMed Central

    2012-01-01

    Background The moss Physcomitrella patens contains C18- as well as C20-polyunsaturated fatty acids that can be metabolized by different enzymes to form oxylipins such as the cyclopentenone cis(+)-12-oxo phytodienoic acid. Mutants defective in the biosynthesis of cyclopentenones showed reduced fertility, aberrant sporophyte morphology and interrupted sporogenesis. The initial step in this biosynthetic route is the conversion of a fatty acid hydroperoxide to an allene oxide. This reaction is catalyzed by allene oxide synthase (AOS) belonging as hydroperoxide lyase (HPL) to the cytochrome P450 family Cyp74. In this study we characterized two AOS from P. patens, PpAOS1 and PpAOS2. Results Our results show that PpAOS1 is highly active with both C18 and C20-hydroperoxy-fatty acid substrates, whereas PpAOS2 is fully active only with C20-substrates, exhibiting trace activity (~1000-fold lower kcat/KM) with C18 substrates. Analysis of products of PpAOS1 and PpHPL further demonstrated that both enzymes have an inherent side activity mirroring the close inter-connection of AOS and HPL catalysis. By employing site directed mutagenesis we provide evidence that single amino acid residues in the active site are also determining the catalytic activity of a 9-/13-AOS – a finding that previously has only been reported for substrate specific 13-AOS. However, PpHPL cannot be converted into an AOS by exchanging the same determinant. Localization studies using YFP-labeled AOS showed that PpAOS2 is localized in the plastid while PpAOS1 may be found in the cytosol. Analysis of the wound-induced cis(+)-12-oxo phytodienoic acid accumulation in PpAOS1 and PpAOS2 single knock-out mutants showed that disruption of PpAOS1, in contrast to PpAOS2, results in a significantly decreased cis(+)-12-oxo phytodienoic acid formation. However, the knock-out mutants of neither PpAOS1 nor PpAOS2 showed reduced fertility, aberrant sporophyte morphology or interrupted sporogenesis. Conclusions Our study

  1. Obituary: James Alfred Van Allen, 1914-2006

    NASA Astrophysics Data System (ADS)

    Ludwig, George H.; McIlwain, Carl Edwin

    2006-12-01

    James Alfred Van Allen, world-renowned space scientist, died 9 August 2006 at the age of ninety-one. He succumbed to heart failure after a ten-week period of declining health. Van Allen served for his entire sixty-seven-year professional career as an amazingly productive researcher, space science spokesman, inspired teacher, and valued colleague. The realization by him and his associates that charged particles are trapped by the Earth's magnetic field began a whole new field of research, magnetospheric physics. Following that initial discovery, he and his associates quickly extended their observations, first to the inner planets, and then to the rest of the planets and beyond. During his tenure at Iowa, he and his group flew instruments on more than sixty successful Earth satellites and planetary spacecraft, including the first missions to the planets Venus, Mars, Jupiter, Saturn, Uranus, and Neptune. Van Allen's lifetime publication list numbers more than 275, of which many are widely-cited, seminal papers. He was the sole author of more than 125 of those papers. Beyond the research laboratory, Van Allen worked energetically throughout his career in establishing space research as a new branch of human inquiry. He was among the most sought-after as a committee member and adviser, working at the highest levels of government, including the White House and Congress, and at all levels of the national and international research establishments. Many presentations in the non-scientific arena helped to bring the exciting discoveries and challenges of space research to the attention of the general public. James Van Allen (Van to his many friends and colleagues) was born on 7 September 1914 on a small farm near Mount Pleasant, Iowa, the second of four sons of Alfred Morris Van Allen and Alma Olney Van Allen. After high school in Mount Pleasant, he entered Iowa Wesleyan College, majoring in physics and graduating summa cum laude. While there, he was introduced to geophysics

  2. A stereotaxic, population-averaged T1w ovine brain atlas including cerebral morphology and tissue volumes.

    PubMed

    Nitzsche, Björn; Frey, Stephen; Collins, Louis D; Seeger, Johannes; Lobsien, Donald; Dreyer, Antje; Kirsten, Holger; Stoffel, Michael H; Fonov, Vladimir S; Boltze, Johannes

    2015-01-01

    Standard stereotaxic reference systems play a key role in human brain studies. Stereotaxic coordinate systems have also been developed for experimental animals including non-human primates, dogs, and rodents. However, they are lacking for other species being relevant in experimental neuroscience including sheep. Here, we present a spatial, unbiased ovine brain template with tissue probability maps (TPM) that offer a detailed stereotaxic reference frame for anatomical features and localization of brain areas, thereby enabling inter-individual and cross-study comparability. Three-dimensional data sets from healthy adult Merino sheep (Ovis orientalis aries, 12 ewes and 26 neutered rams) were acquired on a 1.5 T Philips MRI using a T1w sequence. Data were averaged by linear and non-linear registration algorithms. Moreover, animals were subjected to detailed brain volume analysis including examinations with respect to body weight (BW), age, and sex. The created T1w brain template provides an appropriate population-averaged ovine brain anatomy in a spatial standard coordinate system. Additionally, TPM for gray (GM) and white (WM) matter as well as cerebrospinal fluid (CSF) classification enabled automatic prior-based tissue segmentation using statistical parametric mapping (SPM). Overall, a positive correlation of GM volume and BW explained about 15% of the variance of GM while a positive correlation between WM and age was found. Absolute tissue volume differences were not detected, indeed ewes showed significantly more GM per bodyweight as compared to neutered rams. The created framework including spatial brain template and TPM represent a useful tool for unbiased automatic image preprocessing and morphological characterization in sheep. Therefore, the reported results may serve as a starting point for further experimental and/or translational research aiming at in vivo analysis in this species. PMID:26089780

  3. A stereotaxic, population-averaged T1w ovine brain atlas including cerebral morphology and tissue volumes

    PubMed Central

    Nitzsche, Björn; Frey, Stephen; Collins, Louis D.; Seeger, Johannes; Lobsien, Donald; Dreyer, Antje; Kirsten, Holger; Stoffel, Michael H.; Fonov, Vladimir S.; Boltze, Johannes

    2015-01-01

    Standard stereotaxic reference systems play a key role in human brain studies. Stereotaxic coordinate systems have also been developed for experimental animals including non-human primates, dogs, and rodents. However, they are lacking for other species being relevant in experimental neuroscience including sheep. Here, we present a spatial, unbiased ovine brain template with tissue probability maps (TPM) that offer a detailed stereotaxic reference frame for anatomical features and localization of brain areas, thereby enabling inter-individual and cross-study comparability. Three-dimensional data sets from healthy adult Merino sheep (Ovis orientalis aries, 12 ewes and 26 neutered rams) were acquired on a 1.5 T Philips MRI using a T1w sequence. Data were averaged by linear and non-linear registration algorithms. Moreover, animals were subjected to detailed brain volume analysis including examinations with respect to body weight (BW), age, and sex. The created T1w brain template provides an appropriate population-averaged ovine brain anatomy in a spatial standard coordinate system. Additionally, TPM for gray (GM) and white (WM) matter as well as cerebrospinal fluid (CSF) classification enabled automatic prior-based tissue segmentation using statistical parametric mapping (SPM). Overall, a positive correlation of GM volume and BW explained about 15% of the variance of GM while a positive correlation between WM and age was found. Absolute tissue volume differences were not detected, indeed ewes showed significantly more GM per bodyweight as compared to neutered rams. The created framework including spatial brain template and TPM represent a useful tool for unbiased automatic image preprocessing and morphological characterization in sheep. Therefore, the reported results may serve as a starting point for further experimental and/or translational research aiming at in vivo analysis in this species. PMID:26089780

  4. The EF-hand Ca(2+)-binding protein super-family: a genome-wide analysis of gene expression patterns in the adult mouse brain.

    PubMed

    Girard, F; Venail, J; Schwaller, B; Celio, M R

    2015-05-21

    In mice, 249 putative members of the superfamily of EF-hand domain Ca(2+)-binding proteins, manifesting great diversity in structure, cellular localization and functions have been identified. Three members in particular, namely, calbindin-D28K, calretinin and parvalbumin, are widely used as markers for specific neuronal subpopulations in different regions of the brain. The aim of the present study was to compile a comprehensive atlas of the gene-expression profiles of the entire EF-hand gene superfamily in the murine brain. This was achieved by a meticulous examination of the in-situ hybridization images in the Allen Brain Atlas database. Topographically, our analysis focused on the olfactory bulb, cerebral cortex (barrel cortex in the primary somatosensory area), basal ganglia, hippocampus, amygdala, thalamus, hypothalamus, cerebellum, midbrain, pons and medulla, and on clearly identifiable sub-structures within each of these areas. The expression profiles of four family-members, namely hippocalcin-like 4, neurocalcin-δ, plastin 3 and tescalcin, that have not been hitherto reported, at either the mRNA (in-situ-hybridization) or the protein (immunohistochemical) levels, are now presented for the first time. The fruit of our analysis is a document in which the gene-expression profiles of all members of the EF-hand family genes are compared, and in which future possible neuronal markers for specific cells/brain areas are identified. The assembled information could afford functional clues to investigators, conducive to further experimental pursuit. PMID:25770968

  5. Clarence Allen talks about the responsibilities in earthquake prediction

    USGS Publications Warehouse

    Spall, H.

    1978-01-01

    Dr. Clarence R. Allen is professor of geology and geophysics at the California Institute of Technology. He has been a member of advisory panels to the Executive Office of the President, National Academy of Sciences, National Science Foundation, U.S Geological Survey, UNESCO, California State Mining and Geology Board, and the California Department of Water Resources. Dr. Allen has been President of both the Geological Society of America and the Seismological Society of America (SSA). The title of this interview is based on his presidential address to the SSA in 1976. 

  6. Astronauts Allen and Gemar during extravehicular activity (EVA) training in CCT

    NASA Technical Reports Server (NTRS)

    1994-01-01

    Astronauts Charles D. (Sam) Gemar, and Andrew M. Allen participate in a training exercise at JSC's Crew Compartment Trainer (CCT), located in the Space Vehicle Mockup Facility. Gemar sits inside the airlock as Allen reviews procedures for EVA.

  7. Gold(I)-Catalyzed Hydroarylation of Allenes with Indoles

    PubMed Central

    Toups, Kristina L.; Liu, Gordon T.; Widenhoefer, Ross A.

    2010-01-01

    Reaction of a monosubstituted, 1,3-disubstituted, or tetrasubstituted allene with various indoles catalyzed by a 1:1 mixture of a gold(I) N-heterocyclic carbene complex and AgOTf at room temperature leads to hydroarylation with formation of 3-allyl-indoles in modest to good yield. PMID:20305794

  8. Gold(I)-Catalyzed Hydroarylation of Allenes with Indoles

    PubMed Central

    Toups, Kristina L.; Liu, Gordon T.; Widenhoefer, Ross A.

    2009-01-01

    Reaction of a monosubstituted, 1,3-disubstituted, or tetrasubstituted allene with various indoles catalyzed by a 1:1 mixture of a gold(I) N-heterocyclic carbene complex and AgOTf at room temperature leads to hydroarylation with formation of 3-allyl-indoles in modest to good yield. PMID:17428061

  9. James Van Allen and His Namesake NASA Mission

    NASA Astrophysics Data System (ADS)

    Baker, D. N.; Hoxie, V. C.; Jaynes, A.; Kale, A.; Kanekal, S. G.; Li, X.; Reeves, G. D.; Spence, H. E.

    2013-12-01

    In many ways, James A. Van Allen defined and "invented" modern space research. His example showed the way for government-university partners to pursue basic research that also served important national and international goals. He was a tireless advocate for space exploration and for the role of space science in the spectrum of national priorities.

  10. Van Allen Probes Science Gateway: A Centralized Data Access Point

    NASA Astrophysics Data System (ADS)

    Romeo, G.; Barnes, R. J.; Ukhorskiy, A. Y.; Sotirelis, T.; Stephens, G. K.; Kessel, R.; Potter, M.

    2015-12-01

    The Van Allen Probes Science Gateway acts a centralized interface to the instrument Science Operation Centers (SOCs), provides mission planning tools, and hosts a number of science related activities such as the mission bibliography. Most importantly, the Gateway acts as the primary site for processing and delivering the Van Allen Probes Space Weather data to users. Over the past years, the web-site has been completely redesigned with the focus on easier navigation and improvements of the existing tools such as the orbit plotter, position calculator and magnetic footprint tool. In addition, a new data plotting facility has been added. Based on HTML5, which allows users to interactively plot Van Allen Probes science and space weather data. The user can tailor the tool to display exactly the plot they wish to see and then share this with other users via either a URL or by QR code. Various types of plots can be created, including, simple time series, data plotted as a function of orbital location, and time versus L-Shell, capability of visualizing data from both probes (A & B) on the same plot. In cooperation with all Van Allen Probes Instrument SOCs, the Science Gateway will soon be able to serve higher level data products (Level 3), and to visualize them via the above mentioned HTML5 interface. Users will also be able to create customized CDF files on the fly.

  11. The Evolving Space Weather System—Van Allen Probes Contribution

    NASA Astrophysics Data System (ADS)

    Zanetti, L. J.; Mauk, B. H.; Fox, N. J.; Barnes, R. J.; Weiss, M.; Sotirelis, T. S.; Raouafi, N.-E.; Kessel, R. L.; Becker, H. N.

    2014-10-01

    The overarching goal and purpose of the study of space weather is clear—to understand and address the issues caused by solar disturbances on humans and technological systems. Space weather has evolved in the past few decades from a collection of concerned agencies and researchers to a critical function of the National Weather Service of NOAA. The general effects have also evolved from the well-known telegraph disruptions of the mid-1800s to modern day disturbances of the electric power grid, communications and navigation, human spaceflight and spacecraft systems. The last two items in this list, and specifically the effects of penetrating radiation, were the impetus for the space weather broadcast implemented on NASA's Van Allen Probes' twin pair of satellites, launched in August of 2012 and orbiting directly through Earth's severe radiation belts. The Van Allen Probes mission, formerly the Radiation Belt Storm Probes (RBSP), was renamed soon after launch to honor the discoverer of Earth's radiation belts at the beginning of the space age, the late James Van Allen (the spacecraft themselves are still referred to as RBSP-A and RBSP-B). The Van Allen Probes are one part of NASA's Living With a Star program formulated to advance the scientific understanding of the connection between solar disturbances, the resulting heliospheric conditions, and their effects on the geospace and Earth environment.

  12. 5. Historic American Buildings Survey Harold Allen, Photographer June 1964 ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. Historic American Buildings Survey Harold Allen, Photographer June 1964 TRIPLE STAINED GLASS WINDOWS AND COLUMN SUPPORTING BALCONY (EAST WINDOWS IN SOUTH WALL OF MAIN FLOOR OF AUDITORIUM) - Kehilath Anshe Ma'ariv Synagogue, 3301 South Indiana Avenue, Chicago, Cook County, IL

  13. Automated pipeline for atlas-based annotation of gene expresssion patterns: application to postnatal day 7 mouse brain

    SciTech Connect

    Carson, James P.; Ju, Tao; Bello, Musodiq; Thaller, Christina; Warren, Joe; Kakadiaris, Ioannis; Chiu, Wah; Eichele, Gregor

    2010-02-01

    Abstract As bio-medical images and volumes are being collected at an increasing speed, there is a growing demand for efficient means to organize spatial information for comparative analysis. In many scenarios, such as determining gene expression patterns by in situ hybridization, the images are collected from multiple subjects over a common anatomical region, such as the brain. A fundamental challenge in comparing spatial data from different images is how to account for the shape variations among subjects, which makes direct image-to-image comparison meaningless. In this paper, we describe subdivision meshes as a geometric means to efficiently organize 2D images and 3D volumes collected from different subjects for comparison. The key advantages of a subdivision mesh for this purpose are its light-weight geometric structure and its explicit modeling of anatomical boundaries, which enable efficient and accurate registration. The multi-resolution structure of a subdivision mesh also allows development of fast comparison algorithms among registered images and volumes.

  14. MarsAtlas: A cortical parcellation atlas for functional mapping.

    PubMed

    Auzias, Guillaume; Coulon, Olivier; Brovelli, Andrea

    2016-04-01

    An open question in neuroimaging is how to develop anatomical brain atlases for the analysis of functional data. Here, we present a cortical parcellation model based on macroanatomical information and test its validity on visuomotor-related cortical functional networks. The parcellation model is based on a recently developed cortical parameterization method (Auzias et al., [2013]: IEEE Trans Med Imaging 32:873-887), called HIP-HOP. This method exploits a set of primary and secondary sulci to create an orthogonal coordinate system on the cortical surface. A natural parcellation scheme arises from the axes of the HIP-HOP model running along the fundus of selected sulci. The resulting parcellation scheme, called MarsAtlas, complies with dorsoventral/rostrocaudal direction fields and allows inter-subject matching. To test it for functional mapping, we analyzed a MEG dataset collected from human participants performing an arbitrary visuomotor mapping task. Single-trial high-gamma activity, HGA (60-120 Hz), was estimated using spectral analysis and beamforming techniques at cortical areas arising from a Talairach atlas (i.e., Brodmann areas) and MarsAtlas. Using both atlases, we confirmed that visuomotor associations involve an increase in HGA over the sensorimotor and fronto-parietal network, in addition to medial prefrontal areas. However, MarsAtlas provided: (1) crucial functional information along both the dorsolateral and rostrocaudal direction; (2) an increase in statistical significance. To conclude, our results suggest that the MarsAtlas is a valid anatomical atlas for functional mapping, and represents a potential anatomical framework for integration of functional data arising from multiple techniques such as MEG, intracranial EEG and fMRI. PMID:26813563

  15. Obituary: James Alfred Van Allen, 1914-2006

    NASA Astrophysics Data System (ADS)

    Ludwig, George H.; McIlwain, Carl Edwin

    2006-12-01

    James Alfred Van Allen, world-renowned space scientist, died 9 August 2006 at the age of ninety-one. He succumbed to heart failure after a ten-week period of declining health. Van Allen served for his entire sixty-seven-year professional career as an amazingly productive researcher, space science spokesman, inspired teacher, and valued colleague. The realization by him and his associates that charged particles are trapped by the Earth's magnetic field began a whole new field of research, magnetospheric physics. Following that initial discovery, he and his associates quickly extended their observations, first to the inner planets, and then to the rest of the planets and beyond. During his tenure at Iowa, he and his group flew instruments on more than sixty successful Earth satellites and planetary spacecraft, including the first missions to the planets Venus, Mars, Jupiter, Saturn, Uranus, and Neptune. Van Allen's lifetime publication list numbers more than 275, of which many are widely-cited, seminal papers. He was the sole author of more than 125 of those papers. Beyond the research laboratory, Van Allen worked energetically throughout his career in establishing space research as a new branch of human inquiry. He was among the most sought-after as a committee member and adviser, working at the highest levels of government, including the White House and Congress, and at all levels of the national and international research establishments. Many presentations in the non-scientific arena helped to bring the exciting discoveries and challenges of space research to the attention of the general public. James Van Allen (Van to his many friends and colleagues) was born on 7 September 1914 on a small farm near Mount Pleasant, Iowa, the second of four sons of Alfred Morris Van Allen and Alma Olney Van Allen. After high school in Mount Pleasant, he entered Iowa Wesleyan College, majoring in physics and graduating summa cum laude. While there, he was introduced to geophysics

  16. Van Allen Probes: Resolving Fundamental Physics with Practical Consequences

    NASA Astrophysics Data System (ADS)

    Ukhorskiy, Aleksandr; Sibeck, David; Fox, Nicola; Mauk, Barry; Kessel, Ramona

    The Van Allen Probes twin spacecraft were launched on 30 August 2012 into nearly identical, 1.1 x 5.8 Re elliptical, low inclination (10°) Earth orbits with one of the two spacecraft lapping the other about every 2.5 months. The goal of the mission is to provide understanding of how populations of relativistic electrons and penetrating ions in space form or change in response to variable inputs of energy from the Sun. In this paper we overview the new understanding and discoveries of the Van Allen Probes science investigations since the operational mission began on 1 November 2012, which include formation of multiple coherently ordered structures within the outer electron belt and new persistent “zebra stripes” in the inner electron belt.

  17. Isomer-specific combustion chemistry in allene and propyne flames

    SciTech Connect

    Hansen, Nils; Miller, James A.; Westmoreland, Phillip R.; Kasper, Tina; Kohse-Hoeinghaus, Katharina; Wang, Juan; Cool, Terrill A.

    2009-11-15

    A combined experimental and modeling study is performed to clarify the isomer-specific combustion chemistry in flames fueled by the C{sub 3}H{sub 4} isomers allene and propyne. To this end, mole fraction profiles of several flame species in stoichiometric allene (propyne)/O{sub 2}/Ar flames are analyzed by means of a chemical kinetic model. The premixed flames are stabilized on a flat-flame burner under a reduced pressure of 25 Torr (=33.3 mbar). Quantitative species profiles are determined by flame-sampling molecular-beam mass spectrometry, and the isomer-specific flame compositions are unraveled by employing photoionization with tunable vacuum-ultraviolet synchrotron radiation. The temperature profiles are measured by OH laser-induced fluorescence. Experimental and modeled mole fraction profiles of selected flame species are discussed with respect to the isomer-specific combustion chemistry in both flames. The emphasis is put on main reaction pathways of fuel consumption, of allene and propyne isomerization, and of isomer-specific formation of C{sub 6} aromatic species. The present model includes the latest theoretical rate coefficients for reactions on a C{sub 3}H{sub 5} potential [J.A. Miller, J.P. Senosiain, S.J. Klippenstein, Y. Georgievskii, J. Phys. Chem. A 112 (2008) 9429-9438] and for the propargyl recombination reactions [Y. Georgievskii, S.J. Klippenstein, J.A. Miller, Phys. Chem. Chem. Phys. 9 (2007) 4259-4268]. Larger peak mole fractions of propargyl, allyl, and benzene are observed in the allene flame than in the propyne flame. In these flames virtually all of the benzene is formed by the propargyl recombination reaction. (author)

  18. Van Allen Probes Science Gateway and Space Weather Data Processing

    NASA Astrophysics Data System (ADS)

    Romeo, G.; Barnes, R. J.; Weiss, M.; Fox, N. J.; Mauk, B.; Potter, M.; Kessel, R.

    2014-12-01

    The Van Allen Probes Science Gateway acts as a centralized interface to the instrument Science Operation Centers (SOCs), provides mission planning tools, and hosts a number of science related activities such as the mission bibliography. Most importantly, the Gateway acts as the primary site for processing and delivering the VAP Space Weather data to users. Over the past year, the web-site has been completely redesigned with the focus on easier navigation and improvements of the existing tools such as the orbit plotter, position calculator and magnetic footprint tool. In addition, a new data plotting facility has been added. Based on HTML5, which allows users to interactively plot Van Allen Probes summary and space weather data. The user can tailor the tool to display exactly the plot they wish to see and then share this with other users via either a URL or by QR code. Various types of plots can be created, including simple time series, data plotted as a function of orbital location, and time versus L-Shell. We discuss the new Van Allen Probes Science Gateway and the Space Weather Data Pipeline.

  19. Global empirical models of plasmaspheric hiss using Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Spasojevic, M.; Shprits, Y. Y.; Orlova, K.

    2015-12-01

    Plasmaspheric hiss is a whistler-mode emission that permeates the Earth's plasmasphere and is a significant driver of energetic electron losses through cyclotron resonant pitch angle scattering. The Electric and Magnetic Field Instrument Suite and Integrated Science instrument on the Van Allen Probes mission provides vastly improved measurements of the hiss wave environment including continuous measurements of the wave magnetic field cross-spectral matrix and enhanced low-frequency coverage. Here, we develop empirical models of hiss wave intensity using two years of Van Allen Probes data. First, we describe the construction of the hiss database. Then, we compare the hiss spectral distribution and integrated wave amplitude obtained from Van Allen Probes to those previously extracted from the Combined Release and Radiation Effects Satellite mission. Next, we develop a cubic regression model of the average hiss magnetic field intensity as a function of Kp, L, magnetic latitude, and magnetic local time. We use the full regression model to explore general trends in the data and use insights from the model to develop a simplified model of wave intensity for straightforward inclusion in quasi-linear diffusion calculations of electron scattering rates.

  20. Atlas-based identification of cortical sulci

    NASA Astrophysics Data System (ADS)

    Nowinski, Wieslaw L.; Raphel, Jose K.; Nguyen, Bonnie T.

    1996-04-01

    The identification of cortical sulci is of great importance. In neurosurgical procedures any target in the cranium can be accessed by following the corridors of the sulci and fissures. The fusion of functional and anatomical data also requires the identification of sulci. Several approaches have been proposed for segmentation of the cortical surface and identification of sulci and fissures. Most of them are bottom-up. They work satisfactorily provided that the sulci are well discernible on MRI images, limiting their use to some major sulci and fissures, such as the central sulcus, interhemispheric fissure, or Sylvian fissure. We propose a sulcal model based approach, overcoming some of the above limitations. The sulcal model is derived from two brain atlases: Co-Planar Stereotaxic Atlas of the Human Brain by Talairach- Tournoux (TT), and Atlas of Cerebral Sulci by Ono-Kubik-Abernathey (OKA). The OKA atlas contains 403 patterns for 55 sulci along with their incidence rates of interruptions, side branches, and connections. An electronic version of the OKA atlas was constructed, quantitatively enhanced by placing the sulcal patterns in a stereotactic space. The original patterns from the OKA atlas were digitized, converted into geometric representation, placed in the Talairach stereotactic space, preregistered with the TT atlas, and integrated with a multi- atlas, multi-dimensional neuroimaging system developed by our group. The registration of any atlas with the clinical data automatically registers all atlases with this data. This way the sulcal patterns can be superimposed on data, indicating approximate locations of sulci on images. The approach proposed here provides a simple and real-time registration of the sulcal patterns with clinical data, and an interactive identification and labeling of sulci. This approach assists rather the medical professional, instead of providing a complete automated extraction of a few, primary sulci with certain accuracy, where a

  1. Syntheses of allene-modified derivatives of peridinin toward elucidation of the effective role of the allene function in high energy transfer efficiencies in photosynthesis†

    PubMed Central

    Kajikawa, Takayuki; Aoki, Kazuyoshi; Singh, Ram Shanker; Iwashita, Takashi; Kusumoto, Toshiyuki; Frank, Harry A.; Hashimoto, Hideki

    2013-01-01

    Peridinin is known as the main light-harvesting pigment in photosynthesis in the sea and exhibits exceptionally high energy transfer efficiencies to chlorophyll a. This energy transfer efficiency is thought to be related to the intricate structure of peridinin, which possesses allene and ylidenbutenolide functions in the polyene backbone. There are, however, no studies on the relationship between the structural features of peridinin and its super ability for energy transfer. We then focused on the subjects of why peridinin possesses a unique allene group and how the allene function plays a role in the exceptionally high energy transfer. Toward elucidation of the exact role of the allene function, we now describe the syntheses of three relatively unstable allene-modified derivatives of peridinin along with the results of the Stark spectroscopy of peridinin and the synthesized peridinin derivatives. PMID:19707676

  2. Planetary atlases

    NASA Technical Reports Server (NTRS)

    Batson, R. M.; Inge, J. L.; Morgan, H. F.

    1991-01-01

    Two kinds of planetary map atlases are in production. Atlases of the first kind contain reduced-scale versions of maps in hard-bound books with dimensions of 11 x 14 inches. These new atlases are intended to: (1) provide concise but comprehensive references to the geography of the planets needed by planetary scientists and others; and (2) allow inexpensive access to the planetary map dataset without requiring acquisition and examination of tens or hundreds of full-size map sheets. Two such atlases have been published and a third is in press. Work was begun of an Atlas of the Satellite of the Outer Planets. The second kind of atlas is a popular or semi-technical version designed for commercial publication and distribution. The first edition, The Atlas of the Solar System, is nearly ready for publication. New funding and contracting constraints now make it unlikely that the atlas can be published in the format originally planned. Currently, the possibility of publishing the maps through the U.S. Geological Survey as a series of folios in the I-map series is being explored. The maps are global views of each solid-surface body of the Solar System. Each map shows airbrushed relief, albedo, and, where available, topography. A set of simplified geologic maps is also included. All of the maps are on equal-area projections. Scales are 1:40,000,000 for the Earth and Venus; 1:2,000,000 for the Saturnian satellites Mimas and Enceladus and the Uranian satellite Miranda; 1:100,000 for the Martian satellites, Phobos and Deimos; and 1:10,000,000 for all other bodies.

  3. Supervised method to build an atlas database for multi-atlas segmentation-propagation

    NASA Astrophysics Data System (ADS)

    Shen, Kaikai; Bourgeat, Pierrick; Fripp, Jurgen; Mériaudeau, Fabrice; Ames, David; Ellis, Kathryn A.; Masters, Colin L.; Villemagne, Victor L.; Rowe, Christopher C.; Salvado, Olivier

    2010-03-01

    Multiatlas based segmentation-propagation approaches have been shown to obtain accurate parcelation of brain structures. However, this approach requires a large number of manually delineated atlases, which are often not available. We propose a supervised method to build a population specific atlas database, using the publicly available Internet Brain Segmentation Repository (IBSR). The set of atlases grows iteratively as new atlases are added, so that its segmentation capability may be enhanced in the multiatlas based approach. Using a dataset of 210 MR images of elderly subjects (170 elderly control, 40 Alzheimer's disease) from the Australian Imaging, Biomarkers and Lifestyle (AIBL) study, 40 MR images were segmented to build a population specific atlas database for the purpose of multiatlas segmentation-propagation. The population specific atlases were used to segment the elderly population of 210 MR images, and were evaluated in terms of the agreement among the propagated labels. The agreement was measured by using the entropy H of the probability image produced when fused by voting rule and the partial moment μ2 of the histogram. Compared with using IBSR atlases, the population specific atlases obtained a higher agreement when dealing with images of elderly subjects.

  4. Optimization of large-scale mouse brain connectome via joint evaluation of DTI and neuron tracing data.

    PubMed

    Chen, Hanbo; Liu, Tao; Zhao, Yu; Zhang, Tuo; Li, Yujie; Li, Meng; Zhang, Hongmiao; Kuang, Hui; Guo, Lei; Tsien, Joe Z; Liu, Tianming

    2015-07-15

    Tractography based on diffusion tensor imaging (DTI) data has been used as a tool by a large number of recent studies to investigate structural connectome. Despite its great success in offering unique 3D neuroanatomy information, DTI is an indirect observation with limited resolution and accuracy and its reliability is still unclear. Thus, it is essential to answer this fundamental question: how reliable is DTI tractography in constructing large-scale connectome? To answer this question, we employed neuron tracing data of 1772 experiments on the mouse brain released by the Allen Mouse Brain Connectivity Atlas (AMCA) as the ground-truth to assess the performance of DTI tractography in inferring white matter fiber pathways and inter-regional connections. For the first time in the neuroimaging field, the performance of whole brain DTI tractography in constructing a large-scale connectome has been evaluated by comparison with tracing data. Our results suggested that only with the optimized tractography parameters and the appropriate scale of brain parcellation scheme, can DTI produce relatively reliable fiber pathways and a large-scale connectome. Meanwhile, a considerable amount of errors were also identified in optimized DTI tractography results, which we believe could be potentially alleviated by efforts in developing better DTI tractography approaches. In this scenario, our framework could serve as a reliable and quantitative test bed to identify errors in tractography results which will facilitate the development of such novel tractography algorithms and the selection of optimal parameters. PMID:25953631

  5. Cell-type-specific neuroanatomy of cliques of autism-related genes in the mouse brain.

    PubMed

    Grange, Pascal; Menashe, Idan; Hawrylycz, Michael

    2015-01-01

    Two cliques of genes identified computationally for their high co-expression in the mouse brain according to the Allen Brain Atlas, and for their enrichment in genes related to autism spectrum disorder (ASD), have recently been shown to be highly co-expressed in the cerebellar cortex, compared to what could be expected by chance. Moreover, the expression of these cliques of genes is not homogeneous across the cerebellar cortex, and it has been noted that their expression pattern seems to highlight the granular layer. However, this observation was only made by eye, and recent advances in computational neuroanatomy allow to rank cell types in the mouse brain (characterized by their transcriptome profiles) according to the similarity between their spatial density profiles and the spatial expression profiles of the cliques. We establish by Monte Carlo simulation that with probability at least 99%, the expression profiles of the two cliques are more similar to the density profile of granule cells than 99% of the expression of cliques containing the same number of genes (Purkinje cells also score above 99% in one of the cliques). Thresholding the expression profiles shows that the signal is more intense in the granular layer. Finally, we work out pairs of cell types whose combined expression profiles are more similar to the expression profiles of the cliques than any single cell type. These pairs predominantly consist of one cortical pyramidal cell and one cerebellar cell (which can be either a granule cell or a Purkinje cell). PMID:26074809

  6. Cell-type-specific neuroanatomy of cliques of autism-related genes in the mouse brain

    PubMed Central

    Grange, Pascal; Menashe, Idan; Hawrylycz, Michael

    2015-01-01

    Two cliques of genes identified computationally for their high co-expression in the mouse brain according to the Allen Brain Atlas, and for their enrichment in genes related to autism spectrum disorder (ASD), have recently been shown to be highly co-expressed in the cerebellar cortex, compared to what could be expected by chance. Moreover, the expression of these cliques of genes is not homogeneous across the cerebellar cortex, and it has been noted that their expression pattern seems to highlight the granular layer. However, this observation was only made by eye, and recent advances in computational neuroanatomy allow to rank cell types in the mouse brain (characterized by their transcriptome profiles) according to the similarity between their spatial density profiles and the spatial expression profiles of the cliques. We establish by Monte Carlo simulation that with probability at least 99%, the expression profiles of the two cliques are more similar to the density profile of granule cells than 99% of the expression of cliques containing the same number of genes (Purkinje cells also score above 99% in one of the cliques). Thresholding the expression profiles shows that the signal is more intense in the granular layer. Finally, we work out pairs of cell types whose combined expression profiles are more similar to the expression profiles of the cliques than any single cell type. These pairs predominantly consist of one cortical pyramidal cell and one cerebellar cell (which can be either a granule cell or a Purkinje cell). PMID:26074809

  7. Synergistic Kinetic Resolution and Asymmetric Propargyl Claisen Rearrangement for the Synthesis of Chiral Allenes.

    PubMed

    Liu, Yangbin; Liu, Xiaohua; Hu, Haipeng; Guo, Jing; Xia, Yong; Lin, Lili; Feng, Xiaoming

    2016-03-14

    The asymmetric propargyl Claisen rearrangement provides a convenient entry to chiral allene motifs. Herein, we describe the development of a kinetic resolution and asymmetric rearrangement of racemic propargyl vinyl ethers. This transformation afforded chiral allene products along with the enantiomerically enriched substrate in good yields with excellent diastereo- and enantioselectivity. The complete chirality transfer and facially selective rearrangement enabled the simultaneous construction of an axially chiral allenic unit and a quaternary carbon stereocenter. PMID:26889758

  8. A computational model for the dimerization of allene.

    PubMed

    Skraba, Sarah L; Johnson, Richard P

    2012-12-21

    Computations at the CCSD(T)/6-311+G(d,p)//B3LYP/6-311+G(d,p) level of theory support long-held beliefs that allene dimerization to 1,2-dimethylenecyclobutane proceeds through diradical intermediates rather than a concerted (π)2(s) + (π)2(a) mechanism. Two diastereomeric transition states with orthogonal and skew geometries have been located for C2-C2 dimerization of allene, with predicted barriers of 34.5 and 40.3 kcal/mol, respectively. In dimerization, the outward-facing ligands rotate in a sense opposite to the forming C-C bond. Both transition states lead to nearly orthogonal (D(2)) singlet bisallyl (or tetramethyleneethane) diradical. This diradical has a barrier to planarization of 3.2 kcal/mol through a planar D(2h) geometry and a barrier to methylene rotation of 14.3 kcal/mol. Bisallyl diradical closes through one of four degenerate paths by a conrotatory motion of the methylene groups with a predicted barrier of 15.7 kcal/mol. The low barrier to planarization of bisallyl, and similar barriers for methylene rotation and conrotatory closure are consistent with a stepwise dimerization process which can still maintain stereochemical elements of reactants. These computations support the observation that racemic 1,3-disubstituted allenes, with access to an orthogonal transition state which minimizes steric strain, will dimerize more readily than enantiopure materials and by a mechanism that preferentially bonds M and P enantiomers. PMID:23198916

  9. MRI atlas of the brain

    SciTech Connect

    Bradley, W.G. ); Bydder, G. )

    1990-01-01

    Since most radiologists will start from a basic of familiarity with pathophysiology of disease and a knowledge of cross-sectional imaging (at least in the transaxial plane), they are in a good position to recognize and diagnose many of the abnormalities we can currently see with CT. The appearance of these lesions on MRI is the basis for the majority of the images in this book. Chapters on Tumors, Infarcts and Ischemia, Demyelination and Infection. Hydrocephalus, and Pediatrics feature multiple images displaying the MR appearance of many common lesions with minimal associated text. Instead of focusing on pathophysiology, attention is directed to the variable appearance of these disease states using various MR imaging techniques. Although the MR contrast agent, Gadolinium-DTPA, has similar behavior (physiologically) to meglumine diatrizoate in CT, the MR techniques which result in optimal visualization of enhancing lesions are nonintuitive and are discussed. Similarly, the appearance of flowing blood and CSF and hemorrhage does not follow easily from a pre-existing CT base, therefore additional text has been devoted to these subjects.

  10. The Cerefy Neuroradiology Atlas: a Talairach-Tournoux atlas-based tool for analysis of neuroimages available over the internet.

    PubMed

    Nowinski, Wieslaw L; Belov, Dmitry

    2003-09-01

    The article introduces an atlas-assisted method and a tool called the Cerefy Neuroradiology Atlas (CNA), available over the Internet for neuroradiology and human brain mapping. The CNA contains an enhanced, extended, and fully segmented and labeled electronic version of the Talairach-Tournoux brain atlas, including parcelated gyri and Brodmann's areas. To our best knowledge, this is the first online, publicly available application with the Talairach-Tournoux atlas. The process of atlas-assisted neuroimage analysis is done in five steps: image data loading, Talairach landmark setting, atlas normalization, image data exploration and analysis, and result saving. Neuroimage analysis is supported by a near-real-time, atlas-to-data warping based on the Talairach transformation. The CNA runs on multiple platforms; is able to process simultaneously multiple anatomical and functional data sets; and provides functions for a rapid atlas-to-data registration, interactive structure labeling and annotating, and mensuration. It is also empowered with several unique features, including interactive atlas warping facilitating fine tuning of atlas-to-data fit, navigation on the triplanar formed by the image data and the atlas, multiple-images-in-one display with interactive atlas-anatomy-function blending, multiple label display, and saving of labeled and annotated image data. The CNA is useful for fast atlas-assisted analysis of neuroimage data sets. It increases accuracy and reduces time in localization analysis of activation regions; facilitates to communicate the information on the interpreted scans from the neuroradiologist to other clinicians and medical students; increases the neuroradiologist's confidence in terms of anatomy and spatial relationships; and serves as a user-friendly, public domain tool for neuroeducation. At present, more than 700 users from five continents have subscribed to the CNA. PMID:14527569

  11. Hovering and forward flight energetics in Anna's and Allen's hummingbirds.

    PubMed

    Clark, Christopher James; Dudley, Robert

    2010-01-01

    Aerodynamic theory predicts that the mechanical costs of flight are lowest at intermediate flight speeds; metabolic costs of flight should trend similarly if muscle efficiency is constant. We measured metabolic rates for nine Anna's hummingbirds (Calypte anna) and two male Allen's hummingbirds (Selasphorus sasin) feeding during flight from a free-standing mask over a range of airspeeds. Ten of 11 birds exhibited higher metabolic costs during hovering than during flight at intermediate airspeeds, whereas one individual exhibited comparable costs at hovering and during forward flight up to speeds of approximately 7 m s(-1). Flight costs of all hummingbirds increased at higher airspeeds. Relative to Anna's hummingbirds, Allen's hummingbirds exhibited deeper minima in the power curve, possibly due to higher wing loadings and greater associated costs of induced drag. Although feeding at a mask in an airstream may reduce body drag and, thus, the contributions of parasite power to overall metabolic expenditure, these results suggest that hummingbird power curves are characterized by energetic minima at intermediate speeds relative to hovering costs. PMID:20455711

  12. Observations of Whistler-Mode Chorus with Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Kurth, William; Hospodarsky, George; Santolik, Ondrej; Kletzing, Craig; Bounds, Scott

    2014-10-01

    The Van Allen Probes mission provides an excellent opportunity to observe whistler-mode chorus and its role in the radiation belts. The plasma wave instrument on the two probes, called Waves, includes six identical waveform receivers covering the frequency range from 10 Hz to 12 kHz. The instrument measures three orthogonal magnetic field components and three orthogonal electric field components of waves. This complement supports wave-normal and Poynting flux analyses of chorus as well as other wave modes that interact with radiation belt particles. Extensive use of burst modes provides multicomponent waveforms enabling the study of individual chorus elements, including their substructure. The early-mission publications confirm the importance of chorus to the local acceleration of electrons in the outer radiation belts. The orbital precession of the twin Van Allen Probes through a complete range of local times now allows for a new survey of the distribution of chorus emissions. Hence, we now have the tools to study chorus from the nonlinear growth in chorus element substructures through synoptic studies of the near-equatorial occurrence of chorus out to a distance of approximately 5.8 Earth radii.

  13. Geomagnetic Storms and EMIC waves: Van Allen Probe observations

    NASA Astrophysics Data System (ADS)

    Wang, Dedong; Yuan, Zhigang; Yu, Xiongdong; Huang, Shiyong; Deng, Xiaohua; Zhou, Meng; Li, Haimeng

    2016-04-01

    Electromagnetic Ion Cyclotron (EMIC) waves are believed to play a crucial role in the dynamics of ring current ions and radiation belt electrons, especially during geomagnetic storms. However, there is little consensus on which phase of the storm is more favorable for the generation of EMIC waves. Utilizing the data from magnetometer instrument of EMFISIS suite on board Van Allen Probe A, the occurrences of EMIC waves during geomagnetic storms are investigated in this paper. 76 storms were identified during the period under research, from 8 September 2012 to 30 April 2014, when the apogee of Van Allen Probe A covered all the MLT sectors. 50 of the 76 storms observed 124 EMIC wave events, of which 80 are found in the recovery phase, more than those observed in the main phase. Evolution of the distribution characteristics of EMIC waves respect to L and MLT in different geomagnetic phases is investigated, which is found to be consistent with that of the plasmasphere. These results are different from those derived by the observations of the CRRES satellite. The different results may result from the different orbit coverage of the two different satellite missions or from the different activity level of the magnetosphere during the different periods. Few EMIC waves in the dayside sector during the pre-onset periods are observed. It is implied that, to the generation of EMIC waves, the effect of solar wind dynamic pressure in the inner magnetosphere is not so significant as that in the outer magnetosphere.

  14. Modified Mason-Allen Suture Bridge Technique: A New Suture Bridge Technique with Improved Tissue Holding by the Modified Mason-Allen Stitch

    PubMed Central

    Lee, Bong Gun; Cho, Nam Su

    2012-01-01

    We present a new method of suture bridge technique for medial row fixation using a modified Mason-Allen stitch instead of a horizontal mattress. Medial row configuration of the technique is composed of the simple stitch limb and the modified Mason-Allen stitch limb. The limbs are passed through the tendon by a shuttle relay. The simple stitch limb passes the cuff once and the modified Mason-Allen stitch limb passes three times which creates a rip stop that prevents tendon pull-out. In addition, the Mason-Allen suture bridge configuration is basically a knotless technique which has an advantage of reducing a possibility of strangulation of the rotator cuff tendon, impingement or irritation that may be caused by knot. PMID:22949957

  15. Q & A with Ed Tech Leaders: Interview with Michael W. Allen

    ERIC Educational Resources Information Center

    Shaughnessy, Michael F.

    2014-01-01

    Michael W. Allen, the Chairman and CEO of Allen Interactions, is an architect of interactive multimedia learning and is recognized for his many insights, inventions, and presentations. With over 50 years of experience in e-learning, both in academic and corporate settings, he is known for his role in creating Authorware and overseeing the work of…

  16. Astronaut Andrew M. Allen, mission commander, sets up systems for a television downlink on the

    NASA Technical Reports Server (NTRS)

    1996-01-01

    STS-75 ONBOARD VIEW --- Astronaut Andrew M. Allen, mission commander, sets up systems for a television downlink on the flight deck of the Space Shuttle Columbia. Allen was joined by four other astronauts and an international payload specialist for more than 16 days of research aboard Columbia. The photograph was taken with a 70mm handheld camera.

  17. The Allen telescope array: Commensal and efficient SETI

    NASA Astrophysics Data System (ADS)

    Deboer, David R.

    2006-12-01

    The Allen telescope array (ATA) currently under construction affords the possibility of a dedicated and highly efficient SETI program that may be done commensally with other radio astronomy programs. This symbiosis is important in order to maintain and sustain the long-term effort that may be required in order to achieve success as a positive or null result. The technology that is being exploited is the construction of many small elements that allow large fields-of-view at high sensitivity, the use of ultra-wideband front-ends, and the use of flexible digital “intermediate frequency (IF)” systems. The project is under construction in phases, with the first 32 antennas expected to be functional in the fall of 2004, the next 173 dishes operational early 2006, with plans for 350 antennas total within this decade.

  18. Van Allen Probe Charging During the St. Patrick's Day Event

    NASA Technical Reports Server (NTRS)

    Parker, L. Neergaard; Minow, J. I.

    2015-01-01

    The geomagnetic storms on and around March 17, 2015 marked the largest storms seen in the declining phase of the solar cycle to date. We use the Helium Oxygen Proton Electron (HOPE) mass spectrometer on board the Van Allen Probe - A and B satellites to study in detail the charging effects seen on these spacecraft during this time. Ion particle flux data provides information on the magnitude of the charging events using the ion line charging signature due to low energy ions accelerated by the spacecraft potential. Electron flux observations are used to correlate the charging environment with variations in spacecraft potential through the event. We also investigate the density and temperature of ions and electrons during the time of the charging event.

  19. Ion spectral structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Ferradas, C.; Zhang, J.; Spence, H. E.; Kistler, L. M.; Larsen, B.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.

    2015-12-01

    During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have reported single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). These ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. The HOPE mass spectrometer onboard the Van Allen Probes measures energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of nose-like structures, using 2-years measurements from the HOPE instrument. The results provide important details about the spatial distribution (dependence on geocentric distance), spectral features of the structures (differences among species), and geomagnetic conditions under which these structures occur.

  20. Probabilistic maps of the white matter tracts with known associated functions on the neonatal brain atlas: Application to evaluate longitudinal developmental trajectories in term-born and preterm-born infants.

    PubMed

    Akazawa, Kentaro; Chang, Linda; Yamakawa, Robyn; Hayama, Sara; Buchthal, Steven; Alicata, Daniel; Andres, Tamara; Castillo, Deborrah; Oishi, Kumiko; Skranes, Jon; Ernst, Thomas; Oishi, Kenichi

    2016-03-01

    Diffusion tensor imaging (DTI) has been widely used to investigate the development of the neonatal and infant brain, and deviations related to various diseases or medical conditions like preterm birth. In this study, we created a probabilistic map of fiber pathways with known associated functions, on a published neonatal multimodal atlas. The pathways-of-interest include the superficial white matter (SWM) fibers just beneath the specific cytoarchitectonically defined cortical areas, which were difficult to evaluate with existing DTI analysis methods. The Jülich cytoarchitectonic atlas was applied to define cortical areas related to specific brain functions, and the Dynamic Programming (DP) method was applied to delineate the white matter pathways traversing through the SWM. Probabilistic maps were created for pathways related to motor, somatosensory, auditory, visual, and limbic functions, as well as major white matter tracts, such as the corpus callosum, the inferior fronto-occipital fasciculus, and the middle cerebellar peduncle, by delineating these structures in eleven healthy term-born neonates. In order to characterize maturation-related changes in diffusivity measures of these pathways, the probabilistic maps were then applied to DTIs of 49 healthy infants who were longitudinally scanned at three time-points, approximately five weeks apart. First, we investigated the normal developmental pattern based on 19 term-born infants. Next, we analyzed 30 preterm-born infants to identify developmental patterns related to preterm birth. Last, we investigated the difference in diffusion measures between these groups to evaluate the effects of preterm birth on the development of these functional pathways. Term-born and preterm-born infants both demonstrated a time-dependent decrease in diffusivity, indicating postnatal maturation in these pathways, with laterality seen in the corticospinal tract and the optic radiation. The comparison between term- and preterm

  1. Orion GNC Mitigation Efforts for Van Allen Radiation

    NASA Technical Reports Server (NTRS)

    King, Ellis T.; Jackson, Mark

    2013-01-01

    The Orion Crew Module (CM) is NASA's next generation manned space vehicle, scheduled to return humans to lunar orbit in the coming decade. The Orion avionics and GN&C architectures have progressed through a number of project phases and are nearing completion of a major milestone. The first unmanned test mission, dubbed "Exploration Flight Test One" (EFT-1) is scheduled to launch from NASA Kennedy Space Center late next year and provides the first integrated test of all the vehicle systems, avionics and software. The EFT-1 mission will be an unmanned test flight that includes a high speed re-entry from an elliptical orbit, which will be launched on an expendable launch vehicle (ELV). The ELV will place CM and the ELV upper stage into a low Earth orbit (LEO) for one revolution. After the first LEO, the ELV upper stage will re-ignite and place the combined upper stage/CM into an elliptical orbit whose perigee results in a high energy entry to test CM response in a relatively high velocity, high heating environment. While not producing entry velocities as high as those experienced in returning from a lunar orbit, the trajectory was chosen to provide higher stresses on the thermal protection and guided entry systems, as compared against a lower energy LEO entry. However the required entry geometry with constraints on inclination and landing site result in a trajectory that lingers for many hours in the Van Allen radiation belts. This exposes the vehicle and avionics to much higher levels of high energy proton radiation than a typical LEO or lunar trajectory would encounter. As a result, Van Allen radiation poses a significant risk to the Orion avionics system, and particularly the Flight Control Module (FCM) computers that house the GN&C flight software. The measures taken by the Orion GN&C, Flight Software and Avionics teams to mitigate the risks associated with the Van Allen radiation on EFT-1 are covered in the paper. Background on the Orion avionics subsystem is

  2. Branching Out: Rhodium-Catalyzed Allylation with Alkynes and Allenes.

    PubMed

    Koschker, Philipp; Breit, Bernhard

    2016-08-16

    We present a new and efficient strategy for the atom-economic transformation of both alkynes and allenes to allylic functionalized structures via a Rh-catalyzed isomerization/addition reaction which has been developed in our working group. Our methodology thus grants access to an important structural class valued in modern organic chemistry for both its versatility for further functionalization and the potential for asymmetric synthesis with the construction of a new stereogenic center. This new methodology, inspired by mechanistic investigations by Werner in the late 1980s and based on preliminary work by Yamamoto and Trost, offers an attractive alternative to other established methods for allylic functionalization such as allylic substitution or allylic oxidation. The main advantage of our methodology consists of the inherent atom economy in comparison to allylic oxidation or substitution, which both produce stoichiometric amounts of waste and, in case of the substitution reaction, require prefunctionalization of the starting material. Starting out with the discovery of a highly branched-selective coupling reaction of carboxylic acids with terminal alkynes using a Rh(I)/DPEphos complex as the catalyst system, over the past 5 years we were able to continuously expand upon this chemistry, introducing various (pro)nucleophiles for the selective C-O, C-S, C-N, and C-C functionalization of both alkynes and the double-bond isomeric allenes by choosing the appropriate rhodium/bidentate phosphine catalyst. Thus, valuable compounds such as branched allylic ethers, sulfones, amines, or γ,δ-unsaturated ketones were successfully synthesized in high yields and with a broad substrate scope. Beyond the branched selectivity inherent to rhodium, many of the presented methodologies display additional degrees of selectivity in regard to regio-, diastereo-, and enantioselective transformations, with one example even proceeding via a dynamic kinetic resolution. Many advances

  3. [Book review] Green engineering: environmentally conscious design, by David T. Allen and David R. Shonnard

    USGS Publications Warehouse

    Boustany, R.G.

    2002-01-01

    Review of: Green engineering: Environmentally conscious design / David T. Allen and David R. Shonnard / Prentice-Hall, Inc., One Lake Street, Upper Saddle River, NJ 07458. 2002. 552 pages. ISBN 0-13-061908-6.

  4. Revealing latent value of clinically acquired CTs of traumatic brain injury through multi-atlas segmentation in a retrospective study of 1,003 with external cross-validation

    NASA Astrophysics Data System (ADS)

    Plassard, Andrew J.; Kelly, Patrick D.; Asman, Andrew J.; Kang, Hakmook; Patel, Mayur B.; Landman, Bennett A.

    2015-03-01

    Medical imaging plays a key role in guiding treatment of traumatic brain injury (TBI) and for diagnosing intracranial hemorrhage; most commonly rapid computed tomography (CT) imaging is performed. Outcomes for patients with TBI are variable and difficult to predict upon hospital admission. Quantitative outcome scales (e.g., the Marshall classification) have been proposed to grade TBI severity on CT, but such measures have had relatively low value in staging patients by prognosis. Herein, we examine a cohort of 1,003 subjects admitted for TBI and imaged clinically to identify potential prognostic metrics using a "big data" paradigm. For all patients, a brain scan was segmented with multi-atlas labeling, and intensity/volume/texture features were computed in a localized manner. In a 10-fold crossvalidation approach, the explanatory value of the image-derived features is assessed for length of hospital stay (days), discharge disposition (five point scale from death to return home), and the Rancho Los Amigos functional outcome score (Rancho Score). Image-derived features increased the predictive R2 to 0.38 (from 0.18) for length of stay, to 0.51 (from 0.4) for discharge disposition, and to 0.31 (from 0.16) for Rancho Score (over models consisting only of non-imaging admission metrics, but including positive/negative radiological CT findings). This study demonstrates that high volume retrospective analysis of clinical imaging data can reveal imaging signatures with prognostic value. These targets are suited for follow-up validation and represent targets for future feature selection efforts. Moreover, the increase in prognostic value would improve staging for intervention assessment and provide more reliable guidance for patients.

  5. Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain

    PubMed Central

    Krienen, Fenna M.; Yeo, B. T. Thomas; Ge, Tian; Buckner, Randy L.; Sherwood, Chet C.

    2016-01-01

    The human brain is patterned with disproportionately large, distributed cerebral networks that connect multiple association zones in the frontal, temporal, and parietal lobes. The expansion of the cortical surface, along with the emergence of long-range connectivity networks, may be reflected in changes to the underlying molecular architecture. Using the Allen Institute’s human brain transcriptional atlas, we demonstrate that genes particularly enriched in supragranular layers of the human cerebral cortex relative to mouse distinguish major cortical classes. The topography of transcriptional expression reflects large-scale brain network organization consistent with estimates from functional connectivity MRI and anatomical tracing in nonhuman primates. Microarray expression data for genes preferentially expressed in human upper layers (II/III), but enriched only in lower layers (V/VI) of mouse, were cross-correlated to identify molecular profiles across the cerebral cortex of postmortem human brains (n = 6). Unimodal sensory and motor zones have similar molecular profiles, despite being distributed across the cortical mantle. Sensory/motor profiles were anticorrelated with paralimbic and certain distributed association network profiles. Tests of alternative gene sets did not consistently distinguish sensory and motor regions from paralimbic and association regions: (i) genes enriched in supragranular layers in both humans and mice, (ii) genes cortically enriched in humans relative to nonhuman primates, (iii) genes related to connectivity in rodents, (iv) genes associated with human and mouse connectivity, and (v) 1,454 gene sets curated from known gene ontologies. Molecular innovations of upper cortical layers may be an important component in the evolution of long-range corticocortical projections. PMID:26739559

  6. Rhodium-Catalyzed Cross-Cyclotrimerization and Dimerization of Allenes with Alkynes.

    PubMed

    Sakashita, Kazuki; Shibata, Yu; Tanaka, Ken

    2016-06-01

    It has been established that a cationic rhodium(I)/binap complex catalyzes the cross-cyclotrimerization of two molecules of a monosubstituted allene with one molecule of a functionalized alkyne to give 3,6-dialkylidenecyclohex-1-enes. In contrast, the reactions involving di- or trisubstituted allenes and/or unfunctionalized alkynes afforded cross-dimerization products, substituted dendralenes, through β-hydrogen elimination from the corresponding rhodacycles. PMID:27110668

  7. Iron‐catalyzed Cross‐Coupling of Propargyl Carboxylates and Grignard Reagents: Synthesis of Substituted Allenes

    PubMed Central

    Kessler, Simon N.

    2016-01-01

    Abstract Presented herein is a mild, facile, and efficient iron‐catalyzed synthesis of substituted allenes from propargyl carboxylates and Grignard reagents. Only 1–5 mol % of the inexpensive and environmentally benign [Fe(acac)3] at −20 °C was sufficient to afford a broad range of substituted allenes in excellent yields. The method tolerates a variety of functional groups. PMID:26890161

  8. Diastereoselective Synthesis of the Aminocyclitol Core of Jogyamycin via an Allene Aziridination Strategy

    PubMed Central

    Gerstner, Nels C.; Adams, Christopher S.; Grigg, R. David; Tretbar, Maik; Rigoli, Jared W.; Schomaker, Jennifer M.

    2016-01-01

    Oxidative allene amination provides rapid access to densely functionalized amine-containing stereotriads through highly reactive bicyclic methyleneaziridine intermediates. This strategy has been demonstrated as a viable approach for the construction of the densely functionalized aminocyclitol core of jogyamycin, a natural product with potent antiprotozoal activity. Importantly, the flexibility of oxidative allene amination will enable the syntheses of modified aminocyclitol analogues of the jogyamycin core. PMID:26741730

  9. Microwave-promoted synthesis of bicyclic azocine-β-lactams from bis(allenes).

    PubMed

    Alcaide, Benito; Almendros, Pedro; Aragoncillo, Cristina; Fernández, Israel; Gómez-Campillos, Gonzalo

    2014-08-01

    A metal-free preparation of structurally novel bicyclic azocine-β-lactams has been developed. The first examples accounting for the preparation of eight-membered rings from bis(allenes) in the absence of metals have been achieved by the thermolysis of nonconjugated 2-azetidinone-tethered bis(allenes) on application of microwave irradiation. This selective carbocyclization reaction has been studied experimentally, and additionally, its mechanism has been investigated by a DFT study. PMID:25010752

  10. (Hetero)aromatics from dienynes, enediynes and enyne-allenes.

    PubMed

    Raviola, Carlotta; Protti, Stefano; Ravelli, Davide; Fagnoni, Maurizio

    2016-08-01

    The construction of aromatic rings has become a key objective for organic chemists. While several strategies have been developed for the functionalization of pre-formed aromatic rings, the direct construction of an aromatic core starting from polyunsaturated systems is yet a less explored field. The potential of such reactions in the formation of aromatics increased at a regular pace in the last few years. Nowadays, there are reliable and well-established procedures to prepare polyenic derivatives, such as dienynes, enediynes, enyne-allenes and hetero-analogues. This has stimulated their use in the development of innovative cycloaromatizations. Different examples have recently emerged, suggesting large potential of this strategy in the preparation of (hetero)aromatics. Accordingly, this review highlights the recent advancements in this field and describes the different conditions exploited to trigger the process, including thermal and photochemical activation, as well as the use of transition metal catalysis and the addition of electrophiles/nucleophiles or radical species. PMID:27263976

  11. The Allen Telescope Array Search for Electrostatic Discharges on Mars

    NASA Astrophysics Data System (ADS)

    Anderson, Marin M.; Siemion, Andrew P. V.; Barott, William C.; Bower, Geoffrey C.; Delory, Gregory T.; de Pater, Imke; Werthimer, Dan

    2012-01-01

    The Allen Telescope Array was used to monitor Mars between 2010 March 9 and June 2, over a total of approximately 30 hr, for radio emission indicative of electrostatic discharge. The search was motivated by the report from Ruf et al. of the detection of non-thermal microwave radiation from Mars characterized by peaks in the power spectrum of the kurtosis, or kurtstrum, at 10 Hz, coinciding with a large dust storm event on 2006 June 8. For these observations, we developed a wideband signal processor at the Center for Astronomy Signal Processing and Electronics Research. This 1024 channel spectrometer calculates the accumulated power and power-squared, from which the spectral kurtosis is calculated post-observation. Variations in the kurtosis are indicative of non-Gaussianity in the signal, which can be used to detect variable cosmic signals as well as radio frequency interference (RFI). During the three-month period of observations, dust activity occurred on Mars in the form of small-scale dust storms; however, no signals indicating lightning discharge were detected. Frequent signals in the kurtstrum that contain spectral peaks with an approximate 10 Hz fundamental were seen at both 3.2 and 8.0 GHz, but were the result of narrowband RFI with harmonics spread over a broad frequency range.

  12. THE ALLEN TELESCOPE ARRAY SEARCH FOR ELECTROSTATIC DISCHARGES ON MARS

    SciTech Connect

    Anderson, Marin M.; Siemion, Andrew P. V.; Bower, Geoffrey C.; De Pater, Imke; Barott, William C.; Delory, Gregory T.; Werthimer, Dan

    2012-01-01

    The Allen Telescope Array was used to monitor Mars between 2010 March 9 and June 2, over a total of approximately 30 hr, for radio emission indicative of electrostatic discharge. The search was motivated by the report from Ruf et al. of the detection of non-thermal microwave radiation from Mars characterized by peaks in the power spectrum of the kurtosis, or kurtstrum, at 10 Hz, coinciding with a large dust storm event on 2006 June 8. For these observations, we developed a wideband signal processor at the Center for Astronomy Signal Processing and Electronics Research. This 1024 channel spectrometer calculates the accumulated power and power-squared, from which the spectral kurtosis is calculated post-observation. Variations in the kurtosis are indicative of non-Gaussianity in the signal, which can be used to detect variable cosmic signals as well as radio frequency interference (RFI). During the three-month period of observations, dust activity occurred on Mars in the form of small-scale dust storms; however, no signals indicating lightning discharge were detected. Frequent signals in the kurtstrum that contain spectral peaks with an approximate 10 Hz fundamental were seen at both 3.2 and 8.0 GHz, but were the result of narrowband RFI with harmonics spread over a broad frequency range.

  13. The Allen Telescope Array as Square Kilometer Array Pathfinder

    NASA Astrophysics Data System (ADS)

    Bower, Geoffrey C.

    2007-12-01

    The Allen Telescope Array (ATA) is a new radio interferometer that has begun scientific operations in 2007. Many of the technologies, techniques, and observing modes developed for the ATA are directly applicable to the Square Kilometer Array (SKA). The ATA is a pioneer of the LNSD, which refers to a large number (LN) of small diameter (SD) dishes to create the array. This concept underlies nearly all SKA designs. Other relevant technologies are the offset Gregorian ATA antenna, the ATA wideband log periodic feed, transport of broadband data over fiber optic cables, and flexible digital signal processing electronics. The small dishes of the ATA gives it extraordinary wide-field imaging and survey capability but also require new solutions for calibration and imaging. Real time imaging, rapid response to transients, and thinking telescope technology are also under development. Finally, the ATA is developing commensal observing modes, which enable multiple simultaneous science programs, such as SETI, transient surveys, and HI surveys. Opportunities exist for community members to perform scientific investigations as well as develop techniques and technology for the SKA through use of the ATA.

  14. Active and passive microwave measurements in Hurricane Allen

    NASA Technical Reports Server (NTRS)

    Delnore, V. E.; Bahn, G. S.; Grantham, W. L.; Harrington, R. F.; Jones, W. L.

    1985-01-01

    The NASA Langley Research Center analysis of the airborne microwave remote sensing measurements of Hurricane Allen obtained on August 5 and 8, 1980 is summarized. The instruments were the C-band stepped frequency microwave radiometer and the Ku-band airborne microwave scatterometer. They were carried aboard a NOAA aircraft making storm penetrations at an altitude of 3000 m and are sensitive to rain rate, surface wind speed, and surface wind vector. The wind speed is calculated from the increase in antenna brightness temperature above the estimated calm sea value. The rain rate is obtained from the difference between antenna temperature increases measured at two frequencies, and wind vector is determined from the sea surface normalized radar cross section measured at several azimuths. Comparison wind data were provided from the inertial navigation systems aboard both the C-130 aircraft at 3000 m and a second NOAA aircraft (a P-3) operating between 500 and 1500 m. Comparison rain rate data were obtained with a rain radar aboard the P-3. Evaluation of the surface winds obtained with the two microwave instruments was limited to comparisons with each other and with the flight level winds. Two important conclusions are drawn from these comparisons: (1) the radiometer is accurate when predicting flight level wind speeds and rain; and (2) the scatterometer produces well behaved and consistent wind vectors for the rain free periods.

  15. Connectivity-Based Brain Parcellation

    PubMed Central

    Chen, Rong; JaJa, Joseph; Jin, Yu; Hong, L. Elliot; Herskovits, Edward H.

    2016-01-01

    Defining brain structures of interest is an important preliminary step in brain-connectivity analysis. Researchers interested in connectivity patterns among brain structures typically employ manually delineated volumes of interest, or regions in a readily available atlas, to limit the scope of connectivity analysis to relevant regions. However, most structural brain atlases, and manually delineated volumes of interest, do not take voxel-wise connectivity patterns into consideration, and therefore may not be ideal for anatomic connectivity analysis. We herein propose a method to parcellate the brain into regions of interest based on connectivity. We formulate connectivity-based parcellation as a graph-cut problem, which we solve approximately using a novel multi-class Hopfield network algorithm. We demonstrate the application of this approach using diffusion tensor imaging data from an ongoing study of schizophrenia. Compared to a standard anatomic atlas, the connectivity-based atlas supports better classification performance when distinguishing schizophrenic from normal subjects. Comparing connectivity patterns averaged across the normal and schizophrenic subjects, we note significant systematic differences between the two atlases. PMID:26433899

  16. Analyzing in situ gene expression in the mouse brain with image registration, feature extraction and block clustering

    PubMed Central

    Jagalur, Manjunatha; Pal, Chris; Learned-Miller, Erik; Zoeller, R Thomas; Kulp, David

    2007-01-01

    Background Many important high throughput projects use in situ hybridization and may require the analysis of images of spatial cross sections of organisms taken with cellular level resolution. Projects creating gene expression atlases at unprecedented scales for the embryonic fruit fly as well as the embryonic and adult mouse already involve the analysis of hundreds of thousands of high resolution experimental images mapping mRNA expression patterns. Challenges include accurate registration of highly deformed tissues, associating cells with known anatomical regions, and identifying groups of genes whose expression is coordinately regulated with respect to both concentration and spatial location. Solutions to these and other challenges will lead to a richer understanding of the complex system aspects of gene regulation in heterogeneous tissue. Results We present an end-to-end approach for processing raw in situ expression imagery and performing subsequent analysis. We use a non-linear, information theoretic based image registration technique specifically adapted for mapping expression images to anatomical annotations and a method for extracting expression information within an anatomical region. Our method consists of coarse registration, fine registration, and expression feature extraction steps. From this we obtain a matrix for expression characteristics with rows corresponding to genes and columns corresponding to anatomical sub-structures. We perform matrix block cluster analysis using a novel row-column mixture model and we relate clustered patterns to Gene Ontology (GO) annotations. Conclusion Resulting registrations suggest that our method is robust over intensity levels and shape variations in ISH imagery. Functional enrichment studies from both simple analysis and block clustering indicate that gene relationships consistent with biological knowledge of neuronal gene functions can be extracted from large ISH image databases such as the Allen Brain Atlas [1

  17. Report to users of ATLAS

    SciTech Connect

    Ahmad, I.; Glagola, B.

    1995-05-01

    This report contains discussing in the following areas: Status of the Atlas accelerator; highlights of recent research at Atlas; concept for an advanced exotic beam facility based on Atlas; program advisory committee; Atlas executive committee; and Atlas and ANL physics division on the world wide web.

  18. Multimodal, multidimensional models of mouse brain.

    PubMed

    Mackenzie-Graham, Allan J; Lee, Erh-Fang; Dinov, Ivo D; Yuan, Heng; Jacobs, Russell E; Toga, Arthur W

    2007-01-01

    Naturally occurring mutants and genetically manipulated strains of mice are widely used to model a variety of human diseases. Atlases are an invaluable aid in understanding the impact of such manipulations by providing a standard for comparison and to facilitate the integration of anatomic, genetic, and physiologic observations from multiple subjects and experiments. We have developed digital atlases of the C57BL/6J mouse brain (adult and neonate) as comprehensive frameworks for storing and accessing the myriad types of information about the mouse brain. Along with raw and annotated images, these contain database management systems and a set of tools for comparing information from different techniques and different animals. Each atlas establishes a canonical representation of the mouse brain and provides the tools for the manipulation and analysis of new data. We describe both these atlases and discuss how they may be put to use in organizing and analyzing data from mouse models of epilepsy. PMID:17767578

  19. Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template.

    PubMed

    Majka, Piotr; Chaplin, Tristan A; Yu, Hsin-Hao; Tolpygo, Alexander; Mitra, Partha P; Wójcik, Daniel K; Rosa, Marcello G P

    2016-08-01

    The marmoset is an emerging animal model for large-scale attempts to understand primate brain connectivity, but achieving this aim requires the development and validation of procedures for normalization and integration of results from many neuroanatomical experiments. Here we describe a computational pipeline for coregistration of retrograde tracing data on connections of cortical areas into a 3D marmoset brain template, generated from Nissl-stained sections. The procedure results in a series of spatial transformations that are applied to the coordinates of labeled neurons in the different cases, bringing them into common stereotaxic space. We applied this procedure to 17 injections, placed in the frontal lobe of nine marmosets as part of earlier studies. Visualizations of cortical patterns of connections revealed by these injections are supplied as Supplementary Materials. Comparison between the results of the automated and human-based processing of these cases reveals that the centers of injection sites can be reconstructed, on average, to within 0.6 mm of coordinates estimated by an experienced neuroanatomist. Moreover, cell counts obtained in different areas by the automated approach are highly correlated (r = 0.83) with those obtained by an expert, who examined in detail histological sections for each individual. The present procedure enables comparison and visualization of large datasets, which in turn opens the way for integration and analysis of results from many animals. Its versatility, including applicability to archival materials, may reduce the number of additional experiments required to produce the first detailed cortical connectome of a primate brain. J. Comp. Neurol. 524:2161-2181, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc. PMID:27099164

  20. Regression Models of Atlas Appearance

    PubMed Central

    Rohlfing, Torsten; Sullivan, Edith V.; Pfefferbaum, Adolf

    2010-01-01

    Models of object appearance based on principal components analysis provide powerful and versatile tools in computer vision and medical image analysis. A major shortcoming is that they rely entirely on the training data to extract principal modes of appearance variation and ignore underlying variables (e.g., subject age, gender). This paper introduces an appearance modeling framework based instead on generalized multi-linear regression. The training of regression appearance models is controlled by independent variables. This makes it straightforward to create model instances for specific values of these variables, which is akin to model interpolation. We demonstrate the new framework by creating an appearance model of the human brain from MR images of 36 subjects. Instances of the model created for different ages are compared with average shape atlases created from age-matched sub-populations. Relative tissue volumes vs. age in models are also compared with tissue volumes vs. subject age in the original images. In both experiments, we found excellent agreement between the regression models and the comparison data. We conclude that regression appearance models are a promising new technique for image analysis, with one potential application being the representation of a continuum of mutually consistent, age-specific atlases of the human brain. PMID:19694260

  1. Regression models of atlas appearance.

    PubMed

    Rohlfing, Torsten; Sullivan, Edith V; Pfefferbaum, Adolf

    2009-01-01

    Models of object appearance based on principal components analysis provide powerful and versatile tools in computer vision and medical image analysis. A major shortcoming is that they rely entirely on the training data to extract principal modes of appearance variation and ignore underlying variables (e.g., subject age, gender). This paper introduces an appearance modeling framework based instead on generalized multi-linear regression. The training of regression appearance models is controlled by independent variables. This makes it straightforward to create model instances for specific values of these variables, which is akin to model interpolation. We demonstrate the new framework by creating an appearance model of the human brain from MR images of 36 subjects. Instances of the model created for different ages are compared with average shape atlases created from age-matched sub-populations. Relative tissue volumes vs. age in models are also compared with tissue volumes vs. subject age in the original images. In both experiments, we found excellent agreement between the regression models and the comparison data. We conclude that regression appearance models are a promising new technique for image analysis, with one potential application being the representation of a continuum of mutually consistent, age-specific atlases of the human brain. PMID:19694260

  2. Free software tools for atlas-based volumetric neuroimage analysis

    NASA Astrophysics Data System (ADS)

    Bazin, Pierre-Louis; Pham, Dzung L.; Gandler, William; McAuliffe, Matthew

    2005-04-01

    We describe new and freely available software tools for measuring volumes in subregions of the brain. The method is fast, flexible, and employs well-studied techniques based on the Talairach-Tournoux atlas. The software tools are released as plug-ins for MIPAV, a freely available and user-friendly image analysis software package developed by the National Institutes of Health. Our software tools include a digital Talairach atlas that consists of labels for 148 different substructures of the brain at various scales.

  3. Space Weather data processing and Science Gateway for the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Romeo, G.; Barnes, R. J.; Weiss, M.; Fox, N. J.; Mauk, B.; Potter, M.; Kessel, R.

    2013-12-01

    A near real-time data processing pipeline for the Space Weather broadcast data from the Van Allen Probes is presented. The Van Allen Probes broadcasts a sub-set of the science data in real-time when not downlinking the principal science data. This broadcast is received by several ground stations and relayed to APL in near real time to be ingested into the space weather processing pipeline. This pipeline processes the available level zero space weather data into higher level science data products. These products are made available to the public via the Van Allen Probes Science Gateway website (http://athena.jhuapl.edu). The website acts as pivotal point though which all other instrument SOC's can be accessed. Several other data products (e.g KP/DST indices) and tools (e.g orbit calculator) are made also available to the general public.

  4. Recent Results from the Relativistic Electron Proton Telescope (REPT) onboard the Van Allen Probes Mission

    NASA Astrophysics Data System (ADS)

    Kanekal, S. G.; Baker, D. N.; Elkington, S. R.; Hoxie, V. C.; Li, X.; Spence, H. E.

    2013-05-01

    We describe recent results from the REPT instruments on board Van Allen Probes mission launched on 30 August 2012. The twin spacecraft comprising the Van Allen probes mission are identically instrumented and carry a comprehensive suite of sensors characterizing magnetospheric charged particle populations, electric and magnetic fields and plasma waves. The REPT instruments comprise a well-shielded silicon solid state detector stack, with a state of the art electronics and measure electrons of ~1.5 to > 20 MeV and protons of ~17 to > 100 MeV. The instruments were commissioned 3 days after launch and continue to provide high quality measurements. We describe the Van Allen probes and the REPT instrument and report on the new and unexpected features of the outer zone electron populations observed by REPT.

  5. Underwater views of STS-5 crewmen Lenoir and Allen during EVA training

    NASA Technical Reports Server (NTRS)

    1982-01-01

    Underwater views of STS-5 crewmen Lenoir and Allen during EVA training. In this view, Mission Specialist/Astronaut Joseph P. Allen is in the foreground and Mission Specialist/Astronaut William B. Lenoir is at the top of the photography. Both men are wearing extravehicular mobility unit (EMU) space suits and are weighted down to achieve neutral buoyancy in the 25-ft. deep pool. The background is a full-scale mockup of the Space Shuttle's cargo bay area. Divers assist in the training (35894); Allen goes through a simulation exercise with divers all around (35985); Divers assist the fully suited and tethered Lenoir as he simulates work to be done in the shuttle cargo bay (35986); Lenoir anchors himself to a full-scale mockup of the shuttle orbiter's cargo bay and holds onto a restraining device (35987).

  6. Underwater views of STS-5 crewmen Lenoir and Allen during EVA training

    NASA Technical Reports Server (NTRS)

    1982-01-01

    Underwater views of STS-5 crewmen Lenoir and Allen during EVA training. Mission Specialist/Astronaut Joseph P. Allen, wearing an extravehicular mobility unit (EMU) and weighted down to achieve neutral buoyancy, uses a communication system to talk with fellow Mission Specialist/Astronaut William B. Lenoir (out of frame) during underwater simulation of STS-5 extravehicular activity (EVA) (35899); Both mission specialists coordinate their efforts on a chore near the airlock hatch during training. Lenoir is facing the camera. Their background is a full-scale mock-up of the shuttle payload bay (35900); Lenoir works underwater with a portable foot restraint during training underwater. Allen's backpack or mockup for a portable life support system (PLSS) is seen in one corner of the frame (35901).

  7. Spacecraft-level verification of the Van Allen Probes' RF communication system

    NASA Astrophysics Data System (ADS)

    Crowne, M. J.; Srinivasan, D.; Royster, D.; Weaver, G.; Matlin, D.; Mosavi, N.

    This paper presents the verification process, lessons learned, and selected test results of the radio frequency (RF) communication system of the Van Allen Probes, formerly known as the Radiation Belt Storm Probes (RBSP). The Van Allen Probes mission is investigating the doughnut-shaped regions of space known as the Van Allen radiation belts where the Sun interacts with charged particles trapped in Earth's magnetic field. Understanding this dynamic area that surrounds our planet is important to improving our ability to design spacecraft and missions for reliability and astronaut safety. The Van Allen Probes mission features two nearly identical spacecraft designed, built, and operated by the Johns Hopkins University Applied Physics Laboratory (JHU/APL) for the National Aeronautics and Space Administration (NASA). The RF communication system features the JHU/APL Frontier Radio. The Frontier Radio is a software-defined radio (SDR) designed for spaceborne communications, navigation, radio science, and sensor applications. This mission marks the first spaceflight usage of the Frontier Radio. RF ground support equipment (RF GSE) was developed using a ground station receiver similar to what will be used in flight and whose capabilities provided clarity into RF system performance that was previously not obtained until compatibility testing with the ground segments. The Van Allen Probes underwent EMC, acoustic, vibration, and thermal vacuum testing at the environmental test facilities at APL. During this time the RF communication system was rigorously tested to ensure optimal performance, including system-level testing down to threshold power levels. Compatibility tests were performed with the JHU/APL Satellite Communication Facility (SCF), the Universal Space Network (USN), and the Tracking and Data Relay Satellite System (TDRSS). Successful completion of this program as described in this paper validated the design of the system and demonstrated that it will be able to me

  8. A Century after Van Allen's Birth: Conclusion of Reconnaissance of Radiation Belts in the Solar System

    NASA Astrophysics Data System (ADS)

    Krimigis, S. M.

    2014-12-01

    On May 1, 1958 in the Great Hall of the US National Academy of Sciences, James A. Van Allen, having instrumented Explorer-1 and follow-on satellites with radiation detectors, announced the discovery of intense radiation at high altitudes above Earth. The press dubbed the doughnut-shaped structures "Van Allen Belts" (VAB). Soon thereafter, the search began for VAB at nearby planets. Mariner 2 flew by Venus in 1962 at a distance of 41,000 km, but no radiation was detected. The Mariner 4 mission to Mars did not observe planet-associated increase in radiation, but scaling arguments with Earth's magnetosphere yielded an upper limit to the ratio of magnetic moments of MM/ME < 0.001 (Van Allen et al, 1965). Similarly, the Mariner 5 flyby closer to Venus resulted in a ratio of magnetic moments < 0.001 (Van Allen et al, 1967), dealing a blow to the expectation that all planetary bodies must possess significant VAB. The flyby of Mercury in 1974 by Mariner 10 revealed a weak magnetic field, but the presence of durably trapped higher energy particles remained controversial until MESSENGER in 2011.The first flybys of Jupiter by Pioneers 10, 11 in 1973 and 1974, respectively, measured a plethora of energetic particles in Jupiter's magnetosphere and established the fact that their intensities were rotationally modulated. Later flybys of Jupiter and Saturn by the two Voyagers in 1979 and 1981 revealed that those magnetospheres possessed their own internal plasma source(s) and radiation belts. Subsequent discoveries of Van Allen belts at Uranus and Neptune by Voyager 2 demonstrated that VAB are the rule rather than the exception in planetary environments. We now know from the Voyagers and through Energetic Neutral Atom images from Cassini and IBEX that an immense energetic particle population surrounds the heliosphere itself. Thus, the reconnaissance of radiation belts of our solar system has been completed, some 56 years after the discovery of the Van Allen Belts at Earth.

  9. Public health assessment for petitioned public health assessment, Allen Park Clay Mine, Allen Park, Wayne County, Michigan, Region 5. Cerclis No. MID980568711. Final report

    SciTech Connect

    Not Available

    1994-03-16

    The Allen Park Clay Mine (APCM) landfill is in Wayne County, Michigan, within the city limits of Allen Park. The Ford Motor Company developed a clay mine on the site before 1956. Since 1956, the clay excavations have been backfilled with wastes from the Ford Motor Company Rouge River Plant. Some of the wastes (i.e., electric arc furnace dust and decanter tank tar sludge) are classified by the U.S. Environmental Protection Agency as hazardous. Contaminants, including metals and polycyclic aromatic hydrocarbons (PAHs), have been identified in on-site groundwater, storm water runoff, and sediments. ATSDR could not determine if these contaminants were released from the APCM site. Metals have also been found in on-site air. No completed exposure pathways (ways for contaminants to reach the public) have been identified; however, potential exposure pathways do exist.

  10. Experiments in no-impact control of dingoes: comment on Allen et al. 2013

    PubMed Central

    2014-01-01

    There has been much recent debate in Australia over whether lethal control of dingoes incurs environmental costs, particularly by allowing increase of populations of mesopredators such as red foxes and feral cats. Allen et al. (2013) claim to show in their recent study that suppression of dingo activity by poison baiting does not lead to mesopredator release, because mesopredators are also suppressed by poisoning. We show that this claim is not supported by the data and analysis reported in Allen et al.’s paper. PMID:24558973

  11. Experiments in no-impact control of dingoes: comment on Allen et al. 2013.

    PubMed

    Johnson, Christopher N; Crowther, Mathew S; Dickman, Chris R; Letnic, Michael I; Newsome, Thomas M; Nimmo, Dale G; Ritchie, Euan G; Wallach, Arian D

    2014-01-01

    There has been much recent debate in Australia over whether lethal control of dingoes incurs environmental costs, particularly by allowing increase of populations of mesopredators such as red foxes and feral cats. Allen et al. (2013) claim to show in their recent study that suppression of dingo activity by poison baiting does not lead to mesopredator release, because mesopredators are also suppressed by poisoning. We show that this claim is not supported by the data and analysis reported in Allen et al.'s paper. PMID:24558973

  12. Copper-catalyzed regiodivergent silacarboxylation of allenes with carbon dioxide and a silylborane.

    PubMed

    Tani, Yosuke; Fujihara, Tetsuaki; Terao, Jun; Tsuji, Yasushi

    2014-12-24

    A regiodivergent silacarboxylation of allenes under a CO2 atmosphere with PhMe2Si-B(pin) as a silicon source in the presence of a copper catalyst at 70 °C has been developed. The regioselectivity of the reaction is successfully reversed by the proper choice of ligand; carboxylated vinylsilanes are obtained with rac-Me-DuPhos as the ligand, whereas the use of PCy3 affords carboxylated allylsilanes. Thus, two different carboxylated silanes can be selectively and regiodivergently synthesized from a single allene substrate. PMID:25469703

  13. Cascade Copper-Catalyzed 1,2,3-Trifunctionalization of Terminal Allenes.

    PubMed

    Zhao, Wanxiang; Montgomery, John

    2016-08-10

    A cascade cyanation/diborylation of terminal allenes proceeds efficiently with copper catalysis using bis(pinacolato)diboron (B2Pin2) and N-cyano-N-phenyl-p-methylbenzenesulfonamide (NCTS) as reagents. Mechanistic studies suggest that the process proceeds through cyanoborylation of the substituted π-system of the allene followed by hydroboration of the remaining π-component. A wide array of product derivatives may be accessed through site-selective cross-couplings and N-bromosuccinimide-promoted heteroarylations as well as standard oxidative and reductive conversions of the initially obtained adducts. PMID:27438071

  14. Regiodivergent Intermolecular [3+2] Cycloadditions of Vinyl Aziridines and Allenes: Stereospecific Synthesis of Chiral Pyrrolidines.

    PubMed

    Lin, Tao-Yan; Zhu, Chao-Ze; Zhang, Peichao; Wang, Yidong; Wu, Hai-Hong; Feng, Jian-Jun; Zhang, Junliang

    2016-08-26

    The first rhodium-catalyzed intermolecular [3+2] cycloaddition reaction of vinyl aziridines and allenes for the synthesis of enantioenriched functionalized pyrrolidines was realized. [3+2] cycloaddition with the proximal C=C bond of N-allenamides gave 3-methylene-pyrrolidines in high regio- and diastereoselectivity, whereas, 2-methylene-pyrrolidines were obtained as the major products by the cycloadditions of vinyl aziridines with the distal C=C bond of allenes. Use of readily available starting materials, a broad substrate scope, high selectivity, mild reaction conditions, as well as versatile functionalization of the cycloadducts make this approach very practical and attractive. PMID:27485044

  15. Prediction of tissue-specific effects of gene knockout on apoptosis in different anatomical structures of human brain

    PubMed Central

    2015-01-01

    Background An important issue in the target identification for the drug design is the tissue-specific effect of inhibition of target genes. The task of assessing the tissue-specific effect in suppressing gene activity is especially relevant in the studies of the brain, because a significant variability in gene expression levels among different areas of the brain was well documented. Results A method is proposed for constructing statistical models to predict the potential effect of the knockout of target genes on the expression of genes involved in the regulation of apoptosis in various brain regions. The model connects the expression of the objective group of genes with expression of the target gene by means of machine learning models trained on available expression data. Information about the interactions between target and objective genes is determined by reconstruction of target-centric gene network. STRING and ANDSystem databases are used for the reconstruction of gene networks. The developed models have been used to analyse gene knockout effects of more than 7,500 target genes on the expression of 1,900 objective genes associated with the Gene Ontology category "apoptotic process". The tissue-specific effect was calculated for 12 main anatomical structures of the human brain. Initial values of gene expression in these anatomical structures were taken from the Allen Brain Atlas database. The results of the predictions of the effect of suppressing the activity of target genes on apoptosis, calculated on average for all brain structures, were in good agreement with experimental data on siRNA-inhibition. Conclusions This theoretical paper presents an approach that can be used to assess tissue-specific gene knockout effect on gene expression of the studied biological process in various structures of the brain. Genes that, according to the predictions of the model, have the highest values of tissue-specific effects on the apoptosis network can be considered as

  16. Replacement of two amino acids of 9R-dioxygenase-allene oxide synthase of Aspergillus niger inverts the chirality of the hydroperoxide and the allene oxide.

    PubMed

    Sooman, Linda; Wennman, Anneli; Hamberg, Mats; Hoffmann, Inga; Oliw, Ernst H

    2016-02-01

    The genome of Aspergillus niger codes for a fusion protein (EHA25900), which can be aligned with ~50% sequence identity to 9S-dioxygenase (DOX)-allene oxide synthase (AOS) of Fusarium oxysporum, homologues of the Fusarium and Colletotrichum complexes and with over 62% sequence identity to homologues of Aspergilli, including (DOX)-9R-AOS of Aspergillus terreus. The aims were to characterize the enzymatic activities of EHA25900 and to identify crucial amino acids for the stereospecificity. Recombinant EHA25900 oxidized 18:2n-6 sequentially to 9R-hydroperoxy-10(E),12(Z)-octadecadienoic acid (9R-HPODE) and to a 9R(10)-allene oxide. 9S- and 9R-DOX-AOS catalyze abstraction of the pro-R hydrogen at C-11, but the direction of oxygen insertion differs. A comparison between twelve 9-DOX domains of 9S- and 9R-DOX-AOS revealed conserved amino acid differences, which could contribute to the chirality of products. The Gly616Ile replacement of 9R-DOX-AOS (A. niger) increased the biosynthesis of 9S-HPODE and the 9S(10)-allene oxide, whereas the Phe627Leu replacement led to biosynthesis of 9S-HPODE and the 9S(10)-allene oxide as main products. The double mutant (Gly616Ile, Phe627Leu) formed over 90% of the 9S stereoisomer of HPODE. 9S-HPODE was formed by antarafacial hydrogen abstraction and oxygen insertion, i.e., the original H-abstraction was retained but the product chirality was altered. We conclude that 9R-DOX-AOS can be altered to 9S-DOX-AOS by replacement of two amino acids (Gly616Ile, Phe627Leu) in the DOX domain. PMID:26603902

  17. Enzymatic kinetic resolution of primary allenic alcohols. Application to the total synthesis and stereochemical assignment of striatisporolide A.

    PubMed

    Deska, Jan; Bäckvall, Jan-E

    2009-09-01

    Crude Porcine pancreatic lipase was successfully used for the kinetic resolution of axially chiral primary allenic alcohols providing very high enantioselectivities with E values above 200. This simple access to optically active allenes was applied to the total synthesis of the fungal metabolite (-)-striatisporolide A, allowing its unambiguous stereochemical assignment. PMID:19675888

  18. 76 FR 9636 - Franklin Financial Corporation, Inc., Glen Allen, VA; Approval of Conversion Application

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-18

    ... Office of Thrift Supervision Franklin Financial Corporation, Inc., Glen Allen, VA; Approval of Conversion Application Notice is hereby given that on February 11, 2011, the Office of Thrift Supervision approved the..., NE., Atlanta, Georgia 30309. Dated: February 11, 2011. By the Office of Thrift Supervision. Sandra...

  19. Homoallylic amines by reductive inter- and intramolecular coupling of allenes and nitriles

    PubMed Central

    Manojlovic, Marija D

    2011-01-01

    Summary The one-pot hydrozirconation of allenes and nitriles followed by an in situ transmetalation of the allylzirconocene with dimethylzinc or zinc chloride provides functionalized homoallylic amines. An intramolecular version of this process leads to 3-aminotetrahydrofurans and 3-aminotetrahydropyrans. PMID:21804878

  20. Bis-phosphine allene ligand: coordination chemistry and preliminary applications in catalysis.

    PubMed

    Vanitcha, Avassaya; Damelincourt, Cecilia; Gontard, Geoffrey; Vanthuyne, Nicolas; Mouriès-Mansuy, Virginie; Fensterbank, Louis

    2016-05-21

    A 1,3-bis-diphenylphosphine allene can give rise to new coordination complexes with palladium, platinum and gold metals. These complexes were fully characterized by NMR, HRMS and X-ray diffraction analysis. For gold(i), the corresponding dinuclear complex has been used in a series of diagnostic catalytic reactions and gave promising preliminary results in asymmetric catalysis. PMID:27104618

  1. Astronauts Joseph Allen rides cherry picker over stowage area/work station

    NASA Technical Reports Server (NTRS)

    1984-01-01

    Astronaut Joseph P. Allen rides a cherry picker over to a stowage area/work station to wrap up extravehicular activity (EVA) duties above Earth. The cherry picker is a union of the mobile foot restraint and the remote manipulator system (RMS), controlled from inside Discovery's cabin. The Westar VI/PAM-D satellite is pictured secured in Discovery's cargo bay.

  2. Aryl-Allene Cyclization via a Hg(OTf)2-Catalytic Pathway.

    PubMed

    Yamamoto, Hirofumi; Ueda, Maho; Yamasaki, Naoto; Fujii, Akiyoshi; Sasaki, Ikuo; Igawa, Kazunobu; Kasai, Yusuke; Imagawa, Hiroshi; Nishizawa, Mugio

    2016-06-17

    Hg(OTf)2-catalyzed aryl-allene cyclization accompanied by formation of a quaternary carbon center has been realized. Deuterium-labeling experiments and computational modeling were used to propose a novel catalytic pathway involving direct H-transfer from the aromatic ring to the vinyl mercury moiety followed by mercury 1,2-migration. PMID:27232158

  3. All Together Now: Valerie Allen--U.S. Department of Energy

    ERIC Educational Resources Information Center

    Library Journal, 2005

    2005-01-01

    When Valerie Allen decided she did not want to be a Montessori teacher any longer, she began work on her MLIS. Immediately she learned concepts she could apply to her new job as information specialist for the Department of Energy's (DOE) Office of Scientific and Technical Information (OSTI) at Oak Ridge National Laboratory, TN. While the LIS…

  4. Rh(I)-Catalyzed Insertion of Allenes into C-C Bonds of Benzocyclobutenols.

    PubMed

    Zhao, Chunliang; Liu, Li-Chuan; Wang, Jing; Jiang, Chenran; Zhang, Qing-Wei; He, Wei

    2016-01-15

    Herein we report a Rh(I)-catalyzed two carbon insertion into C-C bonds of benzocyclobutenols by employing symmetrical and unsymmetrical allenes. This reaction provides rapid access to alkylidene tetralins bearing two adjacent stereogenic centers in good yields and diasteroselectivities. PMID:26727276

  5. Magnetospheric Observations from JUNO and the Van Allen Probes on Oct 9, 2013 (Invited)

    NASA Astrophysics Data System (ADS)

    Thorne, R. M.

    2013-12-01

    During the Earth Flyby of JUNO on October 9, 2013, the two Van Allen probes will make observations of magnetospheric waves and particles from a near equatorial orbit with apogee near 5.8 RE in the dusk sector. Both the MagEIS and the RBSPICE instruments on the Van Allen probes will measure the radiation belt and the ring current population over an energy range similar to the JEDI instrument on JUNO, which will be used to provide an important calibration of JEDI during the flyby. Measurements at considerable higher energy obtained from the REPT and RPS instruments on the Van Allen probes can be used to investigate the sensitivity of several instruments and other critical components on JUNO to the type of high-energy penetrating particles, to which the satellite will be exposed after orbital insertion in the Jovian magnetosphere. Several other JUNO instruments such as MAG and WAVES will be operational during the flyby allowing comparison with similar measurement on the Van Allen probes. Highlights of the coordinated observations obtained during the JUNO Earth flyby will be presented.

  6. Precipitation of relativistic electrons of the Van Allen belts into the proton aurora

    SciTech Connect

    Jordanova, Vania K; Miyoshi, Y; Sakaguchi, K; Shiokawa, K; Evans, D S; Connors, M

    2008-01-01

    The Van Allen electron belts consist of two regions encircling the earth in which relativistic electrons are trapped in the earth's magnetic field. Populations of relativistic electrons in the Van Allen belts vary greatly with geomagnetic disturbance and they are a major source of damage to space vehicles. In order to know when and by how much these populations of relativistic electrons increase, it is important to elucidate not only the cause of acceleration of relativistic electrons but also the cause of their loss from the Van Allen belts. Here we show the first evidence that left-hand polarized electromagnetic ion cyclotron (EMIC) plasma waves can cause the loss of relativistic electrons into the atmosphere, on the basis of results of an excellent set of ground and satellite observations showing coincident precipitation of ions with energies of tens of keV and of relativistic electrons into an isolated proton aurora. The proton aurora was produced by precipitation of ions with energies of tens of keV due to EMIC waves near the plasma pause, which is a manifestation of wave-particle interactions. These observations clarify that ions with energies of tens of keV affect the evolution of relativistic electrons in the Van Allen belts via parasitic resonance with EMIC waves, an effect that was first theoretically predicted in the early 1970's.

  7. [4+2] and [4+3] catalytic cycloadditions of allenes.

    PubMed

    López, Fernando; Mascareñas, José L

    2014-05-01

    This feature review describes the development of catalytic [4+2] and [4+3] cycloadditions of allenes, as efficient and practical methodologies for assembling six and seven-membered cyclic systems. The different methodologies have been classified depending on the type of key reactive intermediate that was proposed in the catalytic cycle. PMID:24643377

  8. Efficient access to cis-decalinol frameworks: copper(i)-catalyzed borylative cyclization of allene cyclohexanediones.

    PubMed

    Zhao, Yi-Shuang; Tang, Xiao-Qi; Tao, Jing-Chao; Tian, Ping; Lin, Guo-Qiang

    2016-05-11

    Cu-catalyzed borylative cyclization of allene cyclohexanediones has been described through a tandem β-borylation and intramolecular allylic addition process, affording borylated cis-decalinols with excellent yields and diastereoselectivities. A good enantioselectivity is also achieved in the asymmetric version. The hemiboronate group in the cyclization products could be subjected to several useful transformations. PMID:27116376

  9. A Test of Revised Scales for the Meyer and Allen (1991) Three-Component Commitment Construct.

    ERIC Educational Resources Information Center

    Culpepper, Robert A.

    2000-01-01

    Used confirmatory factor analysis with 2 samples (366 employees and 2,301 nurses) to compare the original and revised versions of the scales developed by J. Meyer and N. Allen (1991) to measure three- component commitment. Results show that substantially improved construct measurement is possible with relatively modest scale revisions. (SLD)

  10. Regioselective Allene Hydrosilylation Catalyzed by NHC Complexes of Nickel and Palladium

    PubMed Central

    Miller, Zachary D.; Li, Wei; Belderrain, Tomás R.; Montgomery, John

    2013-01-01

    Regioselective methods for allene hydrosilylation have been developed, with regioselectivity being governed primarily by choice of metal. Alkenylsilanes are produced via nickel catalysis with larger N-heterocyclic carbene ligands, and allylsilanes are produced via palladium catalysis with smaller N-heterocyclic carbene ligands. These complementary methods allow either regioisomeric product to be obtained with exceptional regiocontrol. PMID:24079389

  11. Free Pulp Transfer for Fingertip Reconstruction—The Algorithm for Complicated Allen Fingertip Defect

    PubMed Central

    Spyropoulou, Georgia-Alexandra; Shih, Hsiang-Shun

    2015-01-01

    Abstract Background: We present a review of all the cases of free toe pulp transfer and an algorithm for application of free pulp transfer in complicated Allen fingertip defect. Methods: Seventeen patients underwent free toe pulp transfer for fingertip reconstruction by the senior author. Twelve cases were Allen type II with oblique pulp defect, 4 were Allen type III, and 1 patient had 2 fingertip injuries classified both as type IV. According to the algorithm presented, for the type III defects where the germinal matrix is still preserved, we use free pulp transfer and nail bed graft to preserve the nail growth instead of toe to hand transfer. For the type IV injuries with multiple defects, a combination of web flap from both big toe and second toe is possible for 1-stage reconstruction. Results: All pulp flaps survived completely. Static 2-point discrimination ranged from 6 to 15 mm (mean: 10.5 mm). No patient presented dysesthesia, hyperesthesia, pain at rest, or cold intolerance. The donor site did not present any nuisances apart from partial skin graft loss in 3 cases. Conclusions: We tried to classify and modify the defects’ reconstruction according to Allen classification. Free toe pulp transfer is a “like with like” reconstruction that provides sensate, glabrous skin with good color and texture match for fingertip trauma, and minimal donor site morbidity compared with traditional toe to hand transfer. PMID:26894009

  12. Complex polycyclic scaffolds by metathesis rearrangement of Himbert arene/allene cycloadducts.

    PubMed

    Lam, Jonathan K; Schmidt, Yvonne; Vanderwal, Christopher D

    2012-11-01

    The intramolecular arene/allene cycloaddition first described 30 years ago by Himbert and Henn permits rapid access to strained polycyclic compounds. Alkene metathesis processes cleanly rearrange appropriately substituted cycloadducts into complex, functional-group-rich polycyclic lactams of potential utility for natural product synthesis and medicinal chemistry. PMID:23067058

  13. Improving the Collection of Student Accounts at Allen County Community College.

    ERIC Educational Resources Information Center

    Geffert, Barbara

    During the past several years, Allen County Community College has experienced a growing number of uncollected student accounts. In an effort to encourage timely payment of student charges, lower the number of students receiving payment deferments, increase cash flow at the beginning of each semester, and reduce the number of bad debts being…

  14. Construction and application of human neonatal DTI atlases

    PubMed Central

    Deshpande, Rajiv; Chang, Linda; Oishi, Kenichi

    2015-01-01

    Atlas-based MRI analysis is one of many analytical methods and is used to investigate typical as well as abnormal neurodevelopment. It has been widely applied to the adult and pediatric populations. Successful applications of atlas-based analysis (ABA) in those cohorts have motivated the creation of a neonatal atlas and parcellation map (PM). The purpose of this review is to discuss the various neonatal diffusion tensor imaging (DTI) atlases that are available for use in ABA, examine how such atlases are constructed, review their applications, and discuss future directions in DTI. Neonatal DTI atlases are created from a template, which can be study-specific or standardized, and merged with the corresponding PM. Study-specific templates can retain higher image registration accuracy, but are usually not applicable across different studies. However, standardized templates can be used to make comparisons among various studies, but may not accurately reflect the anatomies of the study population. Methods such as volume-based template estimation are being developed to overcome these limitations. The applications for ABA, including atlas-based image quantification and atlas-based connectivity analysis, vary from quantifying neurodevelopmental progress to analyzing population differences in groups of neonates. ABA can also be applied to detect pathology related to prematurity at birth or exposure to toxic substances. Future directions for this method include research designed to increase the accuracy of the image parcellation. Methods such as multi-atlas label fusion and multi-modal analysis applied to neonatal DTI currently comprise an active field of research. Moreover, ABA can be used in high-throughput analysis to efficiently process medical images and to assess longitudinal brain changes. The overarching goal of neonatal ABA is application to the clinical setting, to assist with diagnoses, monitor disease progression and, ultimately, outcome prediction. PMID:26578899

  15. New Results About the Earth’s Van Allen Radiation Belts

    NASA Astrophysics Data System (ADS)

    Baker, Daniel

    2015-01-01

    The first great scientific discovery of the Space Age was that the Earth is enshrouded in toroids, or 'belts', of very high-energy magnetically trapped charged particles. Early observations of the radiation environment clearly indicated that the Van Allen belts could be delineated into an inner zone dominated by high-energy protons and an outer zone dominated by high-energy electrons. Subsequent studies showed that electrons in the energy range 100 keV < E< 1 MeV often populated both the inner and outer zones with a pronounced 'slot' region relatively devoid of energetic electrons existing between them. This two-belt structure for the Van Allen moderate-energy electron component was explained as being due to strong interactions of electrons with electromagnetic waves just inside the cold plasma (plasmapause) boundary. The energy distribution, spatial extent and particle species makeup of the Van Allen belts has been subsequently explored by several space missions. However, recent observations by the NASA dual-spacecraft Van Allen Probes mission have revealed wholly unexpected properties of the radiation belts, especially at highly relativistic (E > 2 MeV) and ultra-relativistic (E > 5 MeV) kinetic energies. In this presentation we show using high spatial and temporal resolution data from the Relativistic Electron-Proton Telescope (REPT) experiment on board the Van Allen Probes that multiple belts can exist concurrently and that an exceedingly sharp inner boundary exists for ultra-relativistic electrons. Using additionally available Van Allen Probes data, we demonstrate that these remarkable features of energetic electrons are not due to a physical boundary within Earth's intrinsic magnetic field. Neither is it likely that human-generated electromagnetic transmitter wave fields might produce such effects. Rather, we conclude from these unique measurements that slow natural inward radial diffusion combined with weak, but persistent, wave-particle pitch angle

  16. Intraoperative virtual brain counseling

    NASA Astrophysics Data System (ADS)

    Jiang, Zhaowei; Grosky, William I.; Zamorano, Lucia J.; Muzik, Otto; Diaz, Fernando

    1997-06-01

    Our objective is to offer online real-tim e intelligent guidance to the neurosurgeon. Different from traditional image-guidance technologies that offer intra-operative visualization of medical images or atlas images, virtual brain counseling goes one step further. It can distinguish related brain structures and provide information about them intra-operatively. Virtual brain counseling is the foundation for surgical planing optimization and on-line surgical reference. It can provide a warning system that alerts the neurosurgeon if the chosen trajectory will pass through eloquent brain areas. In order to fulfill this objective, tracking techniques are involved for intra- operativity. Most importantly, a 3D virtual brian environment, different from traditional 3D digitized atlases, is an object-oriented model of the brain that stores information about different brain structures together with their elated information. An object-oriented hierarchical hyper-voxel space (HHVS) is introduced to integrate anatomical and functional structures. Spatial queries based on position of interest, line segment of interest, and volume of interest are introduced in this paper. The virtual brain environment is integrated with existing surgical pre-planning and intra-operative tracking systems to provide information for planning optimization and on-line surgical guidance. The neurosurgeon is alerted automatically if the planned treatment affects any critical structures. Architectures such as HHVS and algorithms, such as spatial querying, normalizing, and warping are presented in the paper. A prototype has shown that the virtual brain is intuitive in its hierarchical 3D appearance. It also showed that HHVS, as the key structure for virtual brain counseling, efficiently integrates multi-scale brain structures based on their spatial relationships.This is a promising development for optimization of treatment plans and online surgical intelligent guidance.

  17. Plasma Wave Measurements in Earth's Magnetosphere by Juno, Van Allen Probes, and Cluster

    NASA Astrophysics Data System (ADS)

    Kurth, W. S.; Hospodarsky, G. B.; Bolton, S. J.; Gurnett, D. A.; Santolik, O.; Kletzing, C.; Thorne, R. M.; Pickett, J. S.

    2013-12-01

    On October 9, 2013, Juno will fly within about 550 km of Earth in the process of executing a gravity assist on its way to its eventual arrival at Jupiter in July 2016. Since this will be the only magnetospheric plasma regime Juno will sample prior to arrival at Jupiter, it presents both engineering and scientific opportunities. One of the scientific opportunities is to make observations in the inner magnetosphere at the same time as the twin Van Allen Probes and Cluster. During the Juno flyby, which is on the dusk side at closest approach, the Van Allen Probes' apoapsis is also in the dusk sector. The Cluster orbits favor comparisons on the nightside after Juno's closest approach. Models of the radiation belts suggest that Juno will traverse both the inner and outer belts, albeit at higher latitudes than the low-inclination Van Allen Probes while the Cluster spacecraft are in a rather high inclination orbit. The Waves instrument on Juno utilizes a single electric dipole antenna and a single search coil sensor for measurements of the electric and magnetic components of plasma waves, consequently it will provide wave spectra and brief bursts of waveforms. The Waves instrument on Van Allen Probes, on the other hand makes triaxial electric and magnetic measurements of plasma waves, hence, can determine the propagation characteristics of waves such as the wave-normal angle, Poynting flux, and polarization characteristics of the waves. The Wideband Instrument on Cluster can be configured to capture single axis (electric or magnetic) waveforms at selected times to coincide with Juno and Van Allen Probes burst observations. We will compare observations of whistler-mode emissions and electron cyclotron harmonic emissions in and near the radiation belts from the vantage points of these spacecraft.

  18. BNL ATLAS Grid Computing

    ScienceCinema

    Michael Ernst

    2010-01-08

    As the sole Tier-1 computing facility for ATLAS in the United States and the largest ATLAS computing center worldwide Brookhaven provides a large portion of the overall computing resources for U.S. collaborators and serves as the central hub for storing,

  19. Language Industries Atlas.

    ERIC Educational Resources Information Center

    Hearn, P. M., Ed.; Button, D. F., Ed.

    This atlas describes the activities of public and private organizations that create the infrastructure within which languages are able to develop and interact in the European Community (EC). It contains over 1,000 descriptions of activities that play a role in shaping the language industries, from a user or provider perspective. The atlas is…

  20. ATLAS ACCEPTANCE TEST

    SciTech Connect

    J.C. COCHRANE; J.V. PARKER; ET AL

    2001-06-01

    The acceptance test program for Atlas, a 23 MJ pulsed power facility for use in the Los Alamos High Energy Density Hydrodynamics program, has been completed. Completion of this program officially releases Atlas from the construction phase and readies it for experiments. Details of the acceptance test program results and of machine capabilities for experiments will be presented.

  1. BNL ATLAS Grid Computing

    SciTech Connect

    Michael Ernst

    2008-10-02

    As the sole Tier-1 computing facility for ATLAS in the United States and the largest ATLAS computing center worldwide Brookhaven provides a large portion of the overall computing resources for U.S. collaborators and serves as the central hub for storing,

  2. Computational analysis of LDDMM for brain mapping

    PubMed Central

    Ceritoglu, Can; Tang, Xiaoying; Chow, Margaret; Hadjiabadi, Darian; Shah, Damish; Brown, Timothy; Burhanullah, Muhammad H.; Trinh, Huong; Hsu, John T.; Ament, Katarina A.; Crocetti, Deana; Mori, Susumu; Mostofsky, Stewart H.; Yantis, Steven; Miller, Michael I.; Ratnanather, J. Tilak

    2013-01-01

    One goal of computational anatomy (CA) is to develop tools to accurately segment brain structures in healthy and diseased subjects. In this paper, we examine the performance and complexity of such segmentation in the framework of the large deformation diffeomorphic metric mapping (LDDMM) registration method with reference to atlases and parameters. First we report the application of a multi-atlas segmentation approach to define basal ganglia structures in healthy and diseased kids' brains. The segmentation accuracy of the multi-atlas approach is compared with the single atlas LDDMM implementation and two state-of-the-art segmentation algorithms—Freesurfer and FSL—by computing the overlap errors between automatic and manual segmentations of the six basal ganglia nuclei in healthy subjects as well as subjects with diseases including ADHD and Autism. The high accuracy of multi-atlas segmentation is obtained at the cost of increasing the computational complexity because of the calculations necessary between the atlases and a subject. Second, we examine the effect of parameters on total LDDMM computation time and segmentation accuracy for basal ganglia structures. Single atlas LDDMM method is used to automatically segment the structures in a population of 16 subjects using different sets of parameters. The results show that a cascade approach and using fewer time steps can reduce computational complexity as much as five times while maintaining reliable segmentations. PMID:23986653

  3. Diabetes Interactive Atlas.

    PubMed

    Kirtland, Karen A; Burrows, Nilka R; Geiss, Linda S

    2014-01-01

    The Diabetes Interactive Atlas is a recently released Web-based collection of maps that allows users to view geographic patterns and examine trends in diabetes and its risk factors over time across the United States and within states. The atlas provides maps, tables, graphs, and motion charts that depict national, state, and county data. Large amounts of data can be viewed in various ways simultaneously. In this article, we describe the design and technical issues for developing the atlas and provide an overview of the atlas' maps and graphs. The Diabetes Interactive Atlas improves visualization of geographic patterns, highlights observation of trends, and demonstrates the concomitant geographic and temporal growth of diabetes and obesity. PMID:24503340

  4. National Atlas maps

    USGS Publications Warehouse

    U.S. Geological Survey

    1991-01-01

    The National Atlas of the United States of America was published by the U.S. Geological Survey in 1970. Its 765 maps and charts are on 335 14- by 19-inch pages. Many of the maps span facing pages. It's worth a quick trip to the library just to leaf through all 335 pages of this book. Rapid scanning of its thematic maps yields rich insights to the geography of issues of continuing national interest. On most maps, the geographic patterns are still valid, though the data are not current. The atlas is out of print, but many of its maps can be purchased separately. Maps that span facing pages in the atlas are printed on one sheet. The maps dated after 1970 are either revisions of original atlas maps, or new maps published in atlas format. The titles of the separate maps are listed here.

  5. Multi-atlas learner fusion: An efficient segmentation approach for large-scale data.

    PubMed

    Asman, Andrew J; Huo, Yuankai; Plassard, Andrew J; Landman, Bennett A

    2015-12-01

    We propose multi-atlas learner fusion (MLF), a framework for rapidly and accurately replicating the highly accurate, yet computationally expensive, multi-atlas segmentation framework based on fusing local learners. In the largest whole-brain multi-atlas study yet reported, multi-atlas segmentations are estimated for a training set of 3464 MR brain images. Using these multi-atlas estimates we (1) estimate a low-dimensional representation for selecting locally appropriate example images, and (2) build AdaBoost learners that map a weak initial segmentation to the multi-atlas segmentation result. Thus, to segment a new target image we project the image into the low-dimensional space, construct a weak initial segmentation, and fuse the trained, locally selected, learners. The MLF framework cuts the runtime on a modern computer from 36 h down to 3-8 min - a 270× speedup - by completely bypassing the need for deformable atlas-target registrations. Additionally, we (1) describe a technique for optimizing the weak initial segmentation and the AdaBoost learning parameters, (2) quantify the ability to replicate the multi-atlas result with mean accuracies approaching the multi-atlas intra-subject reproducibility on a testing set of 380 images, (3) demonstrate significant increases in the reproducibility of intra-subject segmentations when compared to a state-of-the-art multi-atlas framework on a separate reproducibility dataset, (4) show that under the MLF framework the large-scale data model significantly improve the segmentation over the small-scale model under the MLF framework, and (5) indicate that the MLF framework has comparable performance as state-of-the-art multi-atlas segmentation algorithms without using non-local information. PMID:26363845

  6. Two-stage atlas subset selection in multi-atlas based image segmentation

    SciTech Connect

    Zhao, Tingting Ruan, Dan

    2015-06-15

    Purpose: Fast growing access to large databases and cloud stored data presents a unique opportunity for multi-atlas based image segmentation and also presents challenges in heterogeneous atlas quality and computation burden. This work aims to develop a novel two-stage method tailored to the special needs in the face of large atlas collection with varied quality, so that high-accuracy segmentation can be achieved with low computational cost. Methods: An atlas subset selection scheme is proposed to substitute a significant portion of the computationally expensive full-fledged registration in the conventional scheme with a low-cost alternative. More specifically, the authors introduce a two-stage atlas subset selection method. In the first stage, an augmented subset is obtained based on a low-cost registration configuration and a preliminary relevance metric; in the second stage, the subset is further narrowed down to a fusion set of desired size, based on full-fledged registration and a refined relevance metric. An inference model is developed to characterize the relationship between the preliminary and refined relevance metrics, and a proper augmented subset size is derived to ensure that the desired atlases survive the preliminary selection with high probability. Results: The performance of the proposed scheme has been assessed with cross validation based on two clinical datasets consisting of manually segmented prostate and brain magnetic resonance images, respectively. The proposed scheme demonstrates comparable end-to-end segmentation performance as the conventional single-stage selection method, but with significant computation reduction. Compared with the alternative computation reduction method, their scheme improves the mean and medium Dice similarity coefficient value from (0.74, 0.78) to (0.83, 0.85) and from (0.82, 0.84) to (0.95, 0.95) for prostate and corpus callosum segmentation, respectively, with statistical significance. Conclusions: The authors

  7. Isolation and Characterization of Two Geometric Allene Oxide Isomers Synthesized from 9S-Hydroperoxylinoleic Acid by Cytochrome P450 CYP74C3

    PubMed Central

    Brash, Alan R.; Boeglin, William E.; Stec, Donald F.; Voehler, Markus; Schneider, Claus; Cha, Jin K.

    2013-01-01

    Specialized cytochromes P450 or catalase-related hemoproteins transform fatty acid hydroperoxides to allene oxides, highly reactive epoxides leading to cyclopentenones and other products. The stereochemistry of the natural allene oxides is incompletely defined, as are the structural features required for their cyclization. We investigated the transformation of 9S-hydroperoxylinoleic acid with the allene oxide synthase CYP74C3, a reported reaction that unexpectedly produces an allene oxide-derived cyclopentenone. Using biphasic reaction conditions at 0 °C, we isolated the initial products and separated two allene oxide isomers by HPLC at −15 °C. One matched previously described allene oxides in its UV spectrum (λmax 236 nm) and NMR spectrum (defining a 9,10-epoxy-octadec-10,12Z-dienoate). The second was a novel stereoisomer (UV λmax 239 nm) with distinctive NMR chemical shifts. Comparison of NOE interactions of the epoxy proton at C9 in the two allene oxides (and the equivalent NOE experiment in 12,13-epoxy allene oxides) allowed assignment at the isomeric C10 epoxy-ene carbon as Z in the new isomer and the E configuration in all previously characterized allene oxides. The novel 10Z isomer spontaneously formed a cis-cyclopentenone at room temperature in hexane. These results explain the origin of the cyclopentenone, provide insights into the mechanisms of allene oxide cyclization, and define the double bond geometry in naturally occurring allene oxides. PMID:23709224

  8. [Research on Atlas of Viscera].

    PubMed

    Jin, S

    1994-01-01

    Chinese ancient visceral atlas, or anatomical illustrations were derived from Taoist and medical schools through observation in cadavers. During the period from Five-Dynasties to Song, there were several works on visceral atlas, including Yanluo illustration, Atlas of Ou Xifan's visceral atlas of fidelity, Li Jung's Atlas. Among them, there exist relations of transmission-heredity, with gradual improvement. It seems likely that the visceral illustrations in Japanese Wan'an Prescription is the extant illustration of Ou's. After the advent of Atlas of Fidelity visceral atlas was differentiated into 3 different kinds of illustrations, as the Inner Picture (Neijing) of Mingtang Atlas; Neizhao Picture in pulsological works and visceral picture in physical Shenxing picture. Chinese visceral atlas was transmitted to Japan, Korea, Persia, and Europe and exerted some influence on cosmopolitan medicine. PMID:11615236

  9. Visual Search of Neuropil-Enriched RNAs from Brain In Situ Hybridization Data through the Image Analysis Pipeline Hippo-ATESC

    PubMed Central

    Zongaro, Samantha; Bardoni, Barbara; Berto, Gaia; Bianchi, Federico; Molineris, Ivan; Giacobini, Mario; Cagnoni, Stefano; Di Cunto, Ferdinando

    2013-01-01

    Motivation RNA molecules specifically enriched in the neuropil of neuronal cells and in particular in dendritic spines are of great interest for neurobiology in virtue of their involvement in synaptic structure and plasticity. The systematic recognition of such molecules is therefore a very important task. High resolution images of RNA in situ hybridization experiments contained in the Allen Brain Atlas (ABA) represent a very rich resource to identify them and have been so far exploited for this task through human-expert analysis. However, software tools that may automatically address the same objective are not very well developed. Results In this study we describe an automatic method for exploring in situ hybridization data and discover neuropil-enriched RNAs in the mouse hippocampus. We called it Hippo-ATESC (Automatic Texture Extraction from the Hippocampal region using Soft Computing). Bioinformatic validation showed that the Hippo-ATESC is very efficient in the recognition of RNAs which are manually identified by expert curators as neuropil-enriched on the same image series. Moreover, we show that our method can also highlight genes revealed by microdissection-based methods but missed by human visual inspection. We experimentally validated our approach by identifying a non-coding transcript enriched in mouse synaptosomes. The code is freely available on the web at http://ibislab.ce.unipr.it/software/hippo/. PMID:24040258

  10. Out-of-atlas likelihood estimation using multi-atlas segmentation

    PubMed Central

    Asman, Andrew J.; Chambless, Lola B.; Thompson, Reid C.; Landman, Bennett A.

    2013-01-01

    Purpose: Multi-atlas segmentation has been shown to be highly robust and accurate across an extraordinary range of potential applications. However, it is limited to the segmentation of structures that are anatomically consistent across a large population of potential target subjects (i.e., multi-atlas segmentation is limited to “in-atlas” applications). Herein, the authors propose a technique to determine the likelihood that a multi-atlas segmentation estimate is representative of the problem at hand, and, therefore, identify anomalous regions that are not well represented within the atlases. Methods: The authors derive a technique to estimate the out-of-atlas (OOA) likelihood for every voxel in the target image. These estimated likelihoods can be used to determine and localize the probability of an abnormality being present on the target image. Results: Using a collection of manually labeled whole-brain datasets, the authors demonstrate the efficacy of the proposed framework on two distinct applications. First, the authors demonstrate the ability to accurately and robustly detect malignant gliomas in the human brain—an aggressive class of central nervous system neoplasms. Second, the authors demonstrate how this OOA likelihood estimation process can be used within a quality control context for diffusion tensor imaging datasets to detect large-scale imaging artifacts (e.g., aliasing and image shading). Conclusions: The proposed OOA likelihood estimation framework shows great promise for robust and rapid identification of brain abnormalities and imaging artifacts using only weak dependencies on anomaly morphometry and appearance. The authors envision that this approach would allow for application-specific algorithms to focus directly on regions of high OOA likelihood, which would (1) reduce the need for human intervention, and (2) reduce the propensity for false positives. Using the dual perspective, this technique would allow for algorithms to focus on

  11. Generation and evaluation of an ultra-high-field atlas with applications in DBS planning

    NASA Astrophysics Data System (ADS)

    Wang, Brian T.; Poirier, Stefan; Guo, Ting; Parrent, Andrew G.; Peters, Terry M.; Khan, Ali R.

    2016-03-01

    Purpose Deep brain stimulation (DBS) is a common treatment for Parkinson's disease (PD) and involves the use of brain atlases or intrinsic landmarks to estimate the location of target deep brain structures, such as the subthalamic nucleus (STN) and the globus pallidus pars interna (GPi). However, these structures can be difficult to localize with conventional clinical magnetic resonance imaging (MRI), and thus targeting can be prone to error. Ultra-high-field imaging at 7T has the ability to clearly resolve these structures and thus atlases built with these data have the potential to improve targeting accuracy. Methods T1 and T2-weighted images of 12 healthy control subjects were acquired using a 7T MR scanner. These images were then used with groupwise registration to generate an unbiased average template with T1w and T2w contrast. Deep brain structures were manually labelled in each subject by two raters and rater reliability was assessed. We compared the use of this unbiased atlas with two other methods of atlas-based segmentation (single-template and multi-template) for subthalamic nucleus (STN) segmentation on 7T MRI data. We also applied this atlas to clinical DBS data acquired at 1.5T to evaluate its efficacy for DBS target localization as compared to using a standard atlas. Results The unbiased templates provide superb detail of subcortical structures. Through one-way ANOVA tests, the unbiased template is significantly (p <0.05) more accurate than a single-template in atlas-based segmentation and DBS target localization tasks. Conclusion The generated unbiased averaged templates provide better visualization of deep brain nuclei and an increase in accuracy over single-template and lower field strength atlases.

  12. ATLAS solar pointing operations

    NASA Technical Reports Server (NTRS)

    Tyler, C. A.; Zimmerman, C. J.

    1994-01-01

    The ATLAS-series of Spacelab missions are comprised of a diverse group of scientific instruments including instruments for studying the sun and how the sun's energy changes across an eleven-year solar cycle. The ATLAS solar instruments are located on one or more pallets in the Orbiter payload bay and use the Orbiter as a pointing platform for their examinations of the sun. One of the ATLAS instruments contained a sun sensor which allowed scientists and engineers on the ground to see the pointing error of the sun with respect to the instrument and correct for the error based upon the information coming from the ATLAS 1 and ATLAS 2 missions with particular attention given to identifying the sources of pointing discrepancies of the solar instruments and to describe the crew and ground controller procedures that were developed to correct for these discrepancies. The Orbiter pointing behavior from the ATLAS 1 and ATLAS 2 flights presented in this paper can be applied to future flights which use the Orbiter as a pointing platform.

  13. The Millennium Star Atlas

    NASA Astrophysics Data System (ADS)

    Sinnott, R. W.

    1997-08-01

    Derived from Hipparcos and Tycho observations, the Millennium Star Atlas is a set of 1548 charts covering the entire sky to about magnitude 11. It stands apart from all previous printed atlases in completeness to magnitude 10 and in uniformity around the sky. The generous chart scale has made possible a number of innovations never before seen in a star atlas: arrows on high-proper-motion stars, double-star ticks conveying separation and position angle for a specific modern epoch, distance labels for nearby stars, and variable stars coded by amplitude, period, and type. Among the nonstellar objects plotted, more than 8000 galaxies are shown with aspect ratio and orientation.

  14. National uranium resource evaluation: McAllen and Brownsville Quadrangles, Texas

    SciTech Connect

    Charepon, A J; Stauber, A J

    1982-06-01

    The McAllen and Brownsville Quadrangles, Texas, were evaluated to a depth of 1500 m to identify geologic environments and delineate areas favorable for uranium deposits. The environments were selected according to criteria established for the National Uranium Resource Evaluation program. Surface studies included investigations of uranium occurrences described in the literature, of locations of aerial radiometric anomalies, of surface exposures, and of locations of anomalous hydrogeochemical and stream-sediment reconnaissance data and collation of information on uranium exploration. Subsurface evaluation of selected geologic units was accomplished by using electric and gamma-ray well logs to construct maps and construct maps and cross sections. In the McAllen Quadrangle, an environment favorable for Texas roll-type sandstone uranium deposits is identified in 36 areas in the Goliad, Fleming-Oakville, Catahoula-Frio, and Whitsett Formations. All other units in both quadrangles are considered unfavorable.

  15. Arthroscopic Medial Meniscus Posterior Root Fixation Using a Modified Mason-Allen Stitch.

    PubMed

    Chung, Kyu Sung; Ha, Jeong Ku; Ra, Ho Jong; Kim, Jin Goo

    2016-02-01

    A complete radial tear of the meniscus posterior root, which can effectively cause a state of total meniscectomy via loss of hoop tension, requires that the torn root be repaired. Several methods have been used to repair medial meniscus posterior root tears, most of which are based on a simple stitch technique that is known to have stitch-holding strength. We applied a modified version of the Mason-Allen stitch technique, which is recognized as a method for rotator cuff repair surgery because its locking effect overcomes the potential weakness of simple stitches. This article introduces the medial meniscus posterior root tears repair procedure based on a modified Mason-Allen stitch technique in which 2 strands (i.e., 1 simple horizontal and 1 simple vertical stitch) are used. PMID:27073778

  16. Automated determination of electron density from electric field measurements on the Van Allen Probes spacecraft

    NASA Astrophysics Data System (ADS)

    Zhelavskaya, Irina; Kurth, William; Spasojevic, Maria; Shprits, Yuri

    2016-07-01

    We present the Neural-network-based Upper-hybrid Resonance Determination (NURD) algorithm for automatic inference of the electron number density from plasma wave measurements made onboard NASA's Van Allen Probes mission. A feedforward neural network is developed to determine the upper hybrid resonance frequency, f_{uhr}, from electric field measurements, which is then used to calculate the electron number density. In previous missions, the plasma resonance bands were manually identified, and there have been few attempts to do robust, routine automated detections. We describe the design and implementation of the algorithm and perform an initial analysis of the resulting electron number density distribution obtained by applying NURD to 2.5 years of data collected with the EMFISIS instrumentation suite of the Van Allen Probes mission. Densities obtained by NURD are compared to those obtained by another recently developed automated technique and also to an existing empirical plasmasphere and trough density model.

  17. In situ observations of EMIC waves in O+ band by the Van Allen Probe A

    NASA Astrophysics Data System (ADS)

    Yu, Xiongdong; Yuan, Zhigang; Wang, Dedong; Li, Haimeng; Huang, Shiyong; Wang, Zhenzhen; Zheng, Qiao; Zhou, Mingxia; Kletzing, C. A.; Wygant, J. R.

    2015-03-01

    Through polarization and spectra analysis of the magnetic field observed by the Van Allen Probe A, we present two typical cases of O+ band electromagnetic ion cyclotron (EMIC) waves in the outer plasmasphere or plasma trough. Although such O+ band EMIC waves are rarely observed, 18 different events of O+ band EMIC waves (16 events in the outer plasmasphere and two events in the plasma trough) are found from September 2012 to August 2014 with observations of the Van Allen Probe A. We find that the preferred region for the occurrence of O+ band EMIC waves is in L = 2-5 and magnetic local time = 03-13, 19-20, which is in accordance with the occurrence region of O+ ion torus. Therefore, our result suggests that the O+ ion torus in the outer plasmasphere during geomagnetic activities should play an important role in the generation of EMIC waves in O+ band.

  18. Arthroscopic Medial Meniscus Posterior Root Fixation Using a Modified Mason-Allen Stitch

    PubMed Central

    Chung, Kyu Sung; Ha, Jeong Ku; Ra, Ho Jong; Kim, Jin Goo

    2016-01-01

    A complete radial tear of the meniscus posterior root, which can effectively cause a state of total meniscectomy via loss of hoop tension, requires that the torn root be repaired. Several methods have been used to repair medial meniscus posterior root tears, most of which are based on a simple stitch technique that is known to have stitch-holding strength. We applied a modified version of the Mason-Allen stitch technique, which is recognized as a method for rotator cuff repair surgery because its locking effect overcomes the potential weakness of simple stitches. This article introduces the medial meniscus posterior root tears repair procedure based on a modified Mason-Allen stitch technique in which 2 strands (i.e., 1 simple horizontal and 1 simple vertical stitch) are used. PMID:27073778

  19. A Versatile Room-Temperature Route to Di- and Trisubstituted Allenes Using Flow-Generated Diazo Compounds**

    PubMed Central

    Poh, Jian-Siang; Tran, Duc N; Battilocchio, Claudio; Hawkins, Joel M; Ley, Steven V

    2015-01-01

    A copper-catalyzed coupling reaction between flow-generated unstabilized diazo compounds and terminal alkynes provides di- and trisubstituted allenes. This extremely mild and rapid transformation is highly tolerant of several functional groups. PMID:26013774

  20. Whistler-Mode Waves inside Density Ducts Observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Rosborough, S.; Bengtson, M.; Stein, R. L.; Streltsov, A. V.

    2015-12-01

    The Van Allen Probes satellites launched by NASA in 2012 are currently orbiting in Earth's radiation belts collecting data about electromagnetic waves and charged particles in the near-earth space environment. Whistler-mode waves are naturally occurring right-hand polarized, very-low frequency waves (< 30 kHz), that can efficiently interact with the energetic electrons in the earth's radiation belts magnetosphere and remediate them from the magnetosphere by precipitating these particles into the atmosphere. The important property of the whistler-mode waves is that they can be guided by density inhomogeneities extended along the ambient magnetic field and localized in the direction perpendicular to the field. Such density channels can be formed by the density enhancement or depletion and they are called ducts. The primary goal of our research is to find density duct and whistler waves in the data recorded by the Van Allen Probes satellites in the magnetosphere, and to reproduce these data with numerical simulations of time-dependent, two-dimensional electron MHD model. In this paper, we present results from our analysis of the observations performed by the Van Allen Probes satellites on 15 October 2014. Data from the probes show the electric and magnetic fields and plasma density. In this event whistler-mode waves were observed from 01:42 to 01:54 UT inside the localized density enhancement coincided with the flux of energetic electrons. Short time intervals, high concentrated electron density, and electron flux gradient activity make this event very interesting for the investigation. Numerical simulations of the electron MHD model revels reasonable quantitative agreement between numerical results and satellite observations, suggesting that the electromagnetic disturbances recorded by the Van Allen Probes satellites, are the whistler-mode waves indeed.

  1. Shape-based multifeature brain parcellation

    NASA Astrophysics Data System (ADS)

    Nadeem, Saad; Kaufman, Arie

    2016-03-01

    We present a novel approach to parcellate - delineate the anatomical feature (folds, gyri, sulci) boundaries - the brain cortex. Our approach is based on extracting the 3D brain cortical surface mesh from magnetic resonance (MR) images, computing the shape measures (area, mean curvature, geodesic, and travel depths) for this mesh, and delineating the anatomical feature boundaries using these measures. We use angle-area preserving mapping of the cortical surface mesh to a simpler topology (disk or rectangle) to aid in the visualization and delineation of these boundaries. Contrary to commonly used generic 2D brain image atlas-based approaches, we use 3D surface mesh data extracted from a given brain MR imaging data and its specific shape measures for the parcellation. Our method does not require any non-linear registration of a given brain dataset to a generic atlas and hence, does away with the structure similarity assumption critical to the atlas-based approaches. We evaluate our approach using Mindboggle manually labeled brain datasets and achieve the following accuracies: 72.4% for gyri, 78.5% for major sulci, and 98.4% for folds. These results warrant further investigation of this approach as an alternative or as an initialization to the atlas-based approaches.

  2. A neural network approach for identifying particle pitch angle distributions in Van Allen Probes data

    NASA Astrophysics Data System (ADS)

    Souza, V. M.; Vieira, L. E. A.; Medeiros, C.; Da Silva, L. A.; Alves, L. R.; Koga, D.; Sibeck, D. G.; Walsh, B. M.; Kanekal, S. G.; Jauer, P. R.; Rockenbach, M.; Dal Lago, A.; Silveira, M. V. D.; Marchezi, J. P.; Mendes, O.; Gonzalez, W. D.; Baker, D. N.

    2016-04-01

    Analysis of particle pitch angle distributions (PADs) has been used as a means to comprehend a multitude of different physical mechanisms that lead to flux variations in the Van Allen belts and also to particle precipitation into the upper atmosphere. In this work we developed a neural network-based data clustering methodology that automatically identifies distinct PAD types in an unsupervised way using particle flux data. One can promptly identify and locate three well-known PAD types in both time and radial distance, namely, 90° peaked, butterfly, and flattop distributions. In order to illustrate the applicability of our methodology, we used relativistic electron flux data from the whole month of November 2014, acquired from the Relativistic Electron-Proton Telescope instrument on board the Van Allen Probes, but it is emphasized that our approach can also be used with multiplatform spacecraft data. Our PAD classification results are in reasonably good agreement with those obtained by standard statistical fitting algorithms. The proposed methodology has a potential use for Van Allen belt's monitoring.

  3. Spacecraft surface charging within geosynchronous orbit observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Sarno-Smith, Lois K.; Larsen, Brian A.; Skoug, Ruth M.; Liemohn, Michael W.; Breneman, Aaron; Wygant, John R.; Thomsen, Michelle F.

    2016-02-01

    Using the Helium Oxygen Proton Electron (HOPE) and Electric Field and Waves (EFW) instruments from the Van Allen Probes, we explored the relationship between electron energy fluxes in the eV and keV ranges and spacecraft surface charging. We present statistical results on spacecraft charging within geosynchronous orbit by L and MLT. An algorithm to extract the H+ charging line in the HOPE instrument data was developed to better explore intense charging events. Also, this study explored how spacecraft potential relates to electron number density, electron pressure, electron temperature, thermal electron current, and low-energy ion density between 1 and 210 eV. It is demonstrated that it is imperative to use both EFW potential measurements and the HOPE instrument ion charging line for examining times of extreme spacecraft charging of the Van Allen Probes. The results of this study show that elevated electron energy fluxes and high-electron pressures are present during times of spacecraft charging but these same conditions may also occur during noncharging times. We also show noneclipse significant negative charging events on the Van Allen Probes.

  4. Functional analysis of allene oxide cyclase, MpAOC, in the liverwort Marchantia polymorpha.

    PubMed

    Yamamoto, Yusuke; Ohshika, Jun; Takahashi, Tomohiro; Ishizaki, Kimitsune; Kohchi, Takayuki; Matusuura, Hideyuki; Takahashi, Kosaku

    2015-08-01

    12-Oxo-phytodienoic acid (OPDA) is an intermediate in jasmonic acid (JA) biosynthesis. OPDA exerts JA-dependent and JA-independent biological effects; therefore, it is considered a signaling molecule in flowering plants. OPDA is induced by bacterial infection and wounding and inhibits growth in the moss Physcomitrella patens. The functions of OPDA and allene oxide cyclase (AOC) in the liverwort Marchantia polymorpha were explored, which represents the most basal lineage of extant land plants. The analysis of OPDA showed that it is present in M. polymorpha and is increased by wounding. OPDA has been suggested to be involved in the response to environmental stresses. Moreover, OPDA showed growth inhibitory activity in M. polymorpha. Nonetheless JA in M. polymorpha was not found in this study. AOC synthesizes OPDA from an unstable allene oxide. A database search of the M. polymorpha genome identified only a putative gene encoding allene oxide cyclase (MpAOC). Recombinant MpAOC showed AOC activity similar to that in flowering plants. MpAOC was localized to chloroplasts, as in flowering plants. Expression of MpAOC was induced by wounding and OPDA treatment, and positive feedback regulation of OPDA was demonstrated in M. polymorpha. Overexpression of MpAOC increased the endogenous OPDA level and suppressed growth in M. polymorpha. These results indicate the role of OPDA as a signaling molecule regulating growth and the response to wounding in the liverwort M. polymorpha. PMID:25892411

  5. The Van Allen Probes first year of discovery and understanding (Invited)

    NASA Astrophysics Data System (ADS)

    Mauk, B.; Fox, N. J.; Sibeck, D. G.; Kanekal, S. G.; Kessel, R.

    2013-12-01

    The Van Allen Probes twin spacecraft were launched on 30 August 2012 and inserted into nearly identical, 1.1 x 5.8 RE elliptical, low inclination (10°), 9-hour period Earth orbits with one of the two spacecraft lapping the other about every 2.5 months. The discoveries and understandings achieved by the Van Allen Probes science investigations since the operational mission began on 1 November 2012 are all that we had hoped. The probes are discovering new and unanticipated behaviors of the radiation belts, for example coherently ordered multiple structures, and are revealing quantitatively how and why those behaviors occur. The probes are answering definitely outstanding important questions regarding Earth's inner magnetosphere, for example, the extent to which and the processes by which local acceleration contributes to creation of the belts. With its close 2-month coordination with the BARREL mission of opportunity array of Antarctic balloons, the Probes are contributing greatly to our understanding of the causes of radiation belt loss and the relationship between high and low altitude radiation belt phenomena. In this overview presentation we assess the discoveries and findings of the Van Allen Probes mission following its first year of operation, and provide a guide to the activities and achievements anticipated over the next year.

  6. Radition belt dynamics : Recent results from van Allen Probes and future observations from CeREs

    NASA Astrophysics Data System (ADS)

    Kanekal, Shrikanth; O'Brien, Paul; Baker, Daniel N.; Ogasawara, Keiichi; Fennell, Joseph; Christian, Eric; Claudepierre, Seth; Livi, Stefano; Desai, Mihir; Li, Xinlin; Jaynes, Allison; Turner, Drew; Jones, Ashley; Schiller, Quintin

    2016-07-01

    We describe recent observations of the Earth's radiation belts made by instruments on board the Van Allen Probes mission, particularly the Relativistic Electron Proton Telescope (REPT) and the Magnetic Electron Ion spectrometer (MagEIS). These observations have significantly advanced our understanding of terrestrial radiation belt dynamics. The Van Allen Probes mission comprises two identically instrumented spacecraft which were launched 31 August, 2012 into low-inclination lapping equatorial orbits. The orbit periods are about 9 hours, with perigees and apogees of of ~600 km and 5.8 RE respectively. We discuss the new scientific findings of the Van Allen Probes mission regarding the physics of energization and loss of relativistic electrons and their implications for future low-cost missions, especially CubeSats. We describe the CeREs (a Compact Radiation belt Explorer) CubeSat mission currently being built at the Goddard Space Flight Center, and carrying on board, an innovative instrument, the Miniaturized Electron Proton Telescope (MERiT). The MERiT is a compact low-mass low-power instrument measuring electrons from a few keV to tens of MeV in multiple differential channels. MERiT is optimized to measure electron microbursts with a high time resolution of a few milliseconds. We present and discuss possible future scientific contributions from CeREs.

  7. An Impenetrable Barrier to Ultra-Relativistic Electrons in the Van Allen Radiation Belt

    NASA Astrophysics Data System (ADS)

    Baker, Daniel

    2015-04-01

    Early observations indicated that the Earth's Van Allen belts could be delineated into an inner zone dominated by high energy protons and an outer zone dominated by high energy electrons. Subsequent studies showed that moderate-energy electrons (E≲1 MeV) often populate both zones with a deep "slot" region between them. This two-belt structure was explained as being due to strong electron interactions with plasmaspheric hiss just inside the plasmapause boundary with the inner edge of the outer zone corresponding to the minimum plasmapause location. Recent Van Allen Probes observations have revealed unexpected radiation belt morphology, especially at ultra-relativistic (E > 5 MeV) kinetic energies. Here we discuss an exceedingly sharp inner boundary exists for ultra-relativistic electrons. Concurrent data reveal that this barrier for inward electron radial transport is not due to a physical boundary within Earth's intrinsic magnetic field nor is it likely that scattering by human-generated electromagnetic transmitter wave fields would inhibit inward radial diffusion. Rather, we suggest that exceptionally slow natural inward radial diffusion combined with weak, but persistent, wave-particle pitch angle scattering deep inside the Earth's plasmasphere can conspire to create an almost impenetrable barrier through which the most energetic Van Allen belt electrons cannot migrate.

  8. Ion-molecule reactions in unsaturated hydrocarbons - Allene, propyne, diacetylene, and vinylacetylene

    NASA Technical Reports Server (NTRS)

    Anicich, V. G.; Blake, G. A.; Huntress, W. T., Jr.; Kim, J. K.; Mcewan, M. J.

    1984-01-01

    Ion-molecule reactions in allene, propyne, diacetylene, and vinylacetylene (1-buten-3-yne) have been studied at near-thermal energies by the technique of ion cyclotron resonance mass spectrometry. Rate coefficients and branching ratios are reported for the reactions of C3Hn(+) (n = 1-4) with allene and propyne and for the reactions of C4Hn(+) (n = 0-5) with diacetylene and vinylacetylene. Branching ratios are also given for the reactions of C4Hn(+), C5Hn and C6Hn(+) with propyne and for reactions of C6Hn(+) with diacetylene and vinylacetylene. More than 90 percent of the reactive channels lead to product ions having a larger carbon skeleton than the reactant ion. Evidence for ions with the same m/e ratio having differing reactivities was obtained for C3Hn(+), C6H7(+), and C7H7(+). Ion reaction sequences in allene and propyne were followed at higher pressures (0.0001 torr) to investigate secondary, tertiary, and higher order processes.

  9. Spacecraft surface charging within geosynchronous orbit observed by the Van Allen Probes

    DOE PAGESBeta

    Sarno-Smith, Lois K.; Larsen, Brian A.; Skoug, Ruth M.; Liemohn, Michael W.; Breneman, Aaron; Wygant, John R.; Thomsen, Michelle F.

    2016-02-27

    Using the Helium Oxygen Proton Electron (HOPE) and Electric Field and Waves (EFW) instruments from the Van Allen Probes, we explored the relationship between electron energy fluxes in the eV and keV ranges and spacecraft surface charging. We present statistical results on spacecraft charging within geosynchronous orbit by L and MLT. An algorithm to extract the H+ charging line in the HOPE instrument data was developed to better explore intense charging events. Also, this study explored how spacecraft potential relates to electron number density, electron pressure, electron temperature, thermal electron current, and low-energy ion density between 1 and 210 eV.more » It is demonstrated that it is imperative to use both EFW potential measurements and the HOPE instrument ion charging line for examining times of extreme spacecraft charging of the Van Allen Probes. The results of this study show that elevated electron energy fluxes and high-electron pressures are present during times of spacecraft charging but these same conditions may also occur during noncharging times. Furthermore, we also show noneclipse significant negative charging events on the Van Allen Probes.« less

  10. Gradual Diffusion and Punctuated Phase Space Density Enhancements of Highly Relativistic Electrons: Van Allen Probes Observations

    NASA Technical Reports Server (NTRS)

    Baker, D. N.; Jaynes, A. N.; Li, X.; Henderson, M. G.; Kanekal, S. G.; Reeves, G. D.; Spence, H. E.; Claudepierre, S. G.; Fennell, J. F.; Hudson, M. K.

    2014-01-01

    The dual-spacecraft Van Allen Probes mission has provided a new window into mega electron volt (MeV) particle dynamics in the Earth's radiation belts. Observations (up to E (is) approximately 10MeV) show clearly the behavior of the outer electron radiation belt at different timescales: months-long periods of gradual inward radial diffusive transport and weak loss being punctuated by dramatic flux changes driven by strong solar wind transient events. We present analysis of multi-MeV electron flux and phase space density (PSD) changes during March 2013 in the context of the first year of Van Allen Probes operation. This March period demonstrates the classic signatures both of inward radial diffusive energization and abrupt localized acceleration deep within the outer Van Allen zone (L (is) approximately 4.0 +/- 0.5). This reveals graphically that both 'competing' mechanisms of multi-MeV electron energization are at play in the radiation belts, often acting almost concurrently or at least in rapid succession.

  11. Multi-Atlas Based Representations for Alzheimer’s Disease Diagnosis

    PubMed Central

    Min, Rui; Wu, Guorong; Cheng, Jian; Wang, Qian; Shen, Dinggang

    2014-01-01

    Brain morphometry based classification from magnetic resonance (MR) acquisitions has been widely investigated in the diagnosis of Alzheimer’s disease (AD) and its prodromal stage, i.e., mild cognitive impairment (MCI). In the literature, a morphometric representation of brain structures is obtained by spatial normalization of each image into a common space (i.e., a pre-defined atlas) via non-linear registration, thus the corresponding regions in different brains can be compared. However, representations generated from one single atlas may not be sufficient to reveal the underlying anatomical differences between the groups of disease-affected patients and normal controls (NC). In this article, we propose a different methodology, namely the multi-atlas based morphometry, which measures morphometric representations of the same image in different spaces of multiple atlases. Representations generated from different atlases can thus provide the complementary information to discriminate different groups, and also reduce the negative impacts from registration errors. Specifically, each studied subject is registered to multiple atlases, where adaptive regional features are extracted. Then, all features from different atlases are jointly selected by a correlation and relevance based scheme, followed by final classification with the support vector machine (SVM). We have evaluated the proposed method on 459 subjects (97 AD, 117 progressive-MCI (p-MCI), 117 stable-MCI (s-MCI), and 128 NC) from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database, and achieved 91.64% for AD/NC classification and 72.41% for p-MCI/s-MCI classification. Our results clearly demonstrate that the proposed multi-atlas based method can significantly outperform the previous single-atlas based methods. PMID:24753060

  12. Atlas of nuclear medicine

    SciTech Connect

    Van Nostrand, D. ); Baum, S. )

    1988-01-01

    This book contains the proceeding on the atlas of nuclear medicine. Topics covered include: Radionuclide esophageal transit studies, Iodine-131 neck and chest scintigraphy, Indium-111 white blood cell imaging, and Pediatric radionuclide lymphography.

  13. ATLAS Metadata Task Force

    SciTech Connect

    ATLAS Collaboration; Costanzo, D.; Cranshaw, J.; Gadomski, S.; Jezequel, S.; Klimentov, A.; Lehmann Miotto, G.; Malon, D.; Mornacchi, G.; Nemethy, P.; Pauly, T.; von der Schmitt, H.; Barberis, D.; Gianotti, F.; Hinchliffe, I.; Mapelli, L.; Quarrie, D.; Stapnes, S.

    2007-04-04

    This document provides an overview of the metadata, which are needed to characterizeATLAS event data at different levels (a complete run, data streams within a run, luminosity blocks within a run, individual events).

  14. General Dynamics Atlas family

    NASA Astrophysics Data System (ADS)

    Oates, James

    Developments concerning the Atlas family of launch vehicles over the last three or four years are summarized. Attention is given to the center of gravity, load factors, acoustics, pyroshock, low-frequency sinusoidal vibration, and high-frequency random vibration.

  15. ATLAS accelerator laboratory report

    SciTech Connect

    Den Hartog, P.

    1986-01-01

    The operation of the ATLAS Accelerator is reported. Modifications are reported, including the installation of conductive tires for the Pelletron chain pulleys, installation of a new high frequency sweeper system at the entrance to the linac, and improvements to the rf drive ports of eight resonators to correct failures in the thermally conductive ceramic insulators. Progress is reported on the positive-ion injector upgrade for ATLAS. Also reported are building modifications and possible new uses for the tandem injector. (LEW)

  16. Atlas Skills for Learning Rather than Learning Atlas Skills.

    ERIC Educational Resources Information Center

    Carswell, R. J. B.

    1986-01-01

    Presents a model for visual learning and describes an approach to skills instruction which aids students in using atlases. Maintains that teachers must help students see atlases as tools capable of providing useful information rather than experiencing atlas learning as an empty exercise with little relevance to their lives. (JDH)

  17. ATLAS@AWS

    NASA Astrophysics Data System (ADS)

    Gehrcke, Jan-Philip; Kluth, Stefan; Stonjek, Stefan

    2010-04-01

    We show how the ATLAS offline software is ported on the Amazon Elastic Compute Cloud (EC2). We prepare an Amazon Machine Image (AMI) on the basis of the standard ATLAS platform Scientific Linux 4 (SL4). Then an instance of the SLC4 AMI is started on EC2 and we install and validate a recent release of the ATLAS offline software distribution kit. The installed software is archived as an image on the Amazon Simple Storage Service (S3) and can be quickly retrieved and connected to new SL4 AMI instances using the Amazon Elastic Block Store (EBS). ATLAS jobs can then configure against the release kit using the ATLAS configuration management tool (cmt) in the standard way. The output of jobs is exported to S3 before the SL4 AMI is terminated. Job status information is transferred to the Amazon SimpleDB service. The whole process of launching instances of our AMI, starting, monitoring and stopping jobs and retrieving job output from S3 is controlled from a client machine using python scripts implementing the Amazon EC2/S3 API via the boto library working together with small scripts embedded in the SL4 AMI. We report our experience with setting up and operating the system using standard ATLAS job transforms.

  18. [A study on Horace N. Allen's medicine and recognition of Korean body].

    PubMed

    Lee, Young Ah

    2011-12-31

    Je Jung Won was the first modern-style Government hospital built by the Korean King Ko-Jong in April 1885, and it was the medical missionary Horace Newton Allen(1858~1932) who made one of the greatest contributions to the establishment of the hospital. Allen was an American missionary. He graduated from Ohio Wesleyan University with a degree in theology in 1881, and completed one-yearcourse at Miami Medical College. In Korea and America he worked as a physician, a missionary, an American diplomatic minister to Korea and a Korean minister's secretary to America. While acting as a mediator between Korea and America, he knew and recorded the domestic and foreign situation of Korea during Gaehwagi(the civilized and enlightened age). Thus to study him is to understand Korea's Gaehwagi as well as to research American medical missionaries. During his stay in Korea(1884~1905), Allen steadily wrote diaries and letters about Korean politics, diplomacy, society, culture, and medicine. Thus his public/private record through diaries and letters(the quantity of these materials amounts to several thousands) supplements the Korean early modern era's historical record. However, until now these materials have received little scholarly attention from researchers except for a few historians of missionary work between Korea and America, or of Korean modern medicine. I intended to use these materials to suggest a new perspective on the study of Korean Gaehwagi. Allen, along with John W. Heron, who came to Seoul on June 21st 1885, treated about 10,460 Korean patients in the first year of the opening of JeJungWon. They made "the first annual report of the Korean Government Hospital". This report explained how Allen and Heron regarded and treated Korean patients. Allen's diaries, letters and other writings offer a realistic view of how the western people actually recognized the Korean people at that time. As a western doctor, Allen had an ambivalent attitude toward Korean medical concepts

  19. Atlas Mountain Range, Mali, Africa

    NASA Technical Reports Server (NTRS)

    1992-01-01

    ATLAS pallets are backdropped against the Atlas Mountains (31.0N, 1.0W). ATLAS is an acronym for ATmospheric Laboratory for Applications and Science. Taken from a point over Mali, in the western Sahara, the northwest looking view shows dunes in the Iguidi dune sea and colors characteristic of the Saharan side of the Atlas Mountains. The edge of a large sandstorm, that transported sand and dust to Yugoslavia and beyond, can also be seen.

  20. Report to users of ATLAS

    SciTech Connect

    Ahmad, I.; Glagola, B.

    1997-03-01

    This report covers the following topics: (1) status of the ATLAS accelerator; (2) progress in R and D towards a proposal for a National ISOL Facility; (3) highlights of recent research at ATLAS; (4) the move of gammasphere from LBNL to ANL; (5) Accelerator Target Development laboratory; (6) Program Advisory Committee; (7) ATLAS User Group Executive Committee; and (8) ATLAS user handbook available in the World Wide Web. A brief summary is given for each topic.

  1. Measuring specific receptor binding of a PET radioligand in human brain without pharmacological blockade: The genomic plot

    PubMed Central

    Veronese, Mattia; Zanotti-Fregonara, Paolo; Rizzo, Gaia; Bertoldo, Alessandra; Innis, Robert B.; Turkheimer, Federico E.

    2016-01-01

    PET studies allow in vivo imaging of the density of brain receptor species. The PET signal, however, is the sum of the fraction of radioligand that is specifically bound to the target receptor and the non-displaceable fraction (i.e. the non-specifically bound radioligand plus the free ligand in tissue). Therefore, measuring the non-displaceable fraction, which is generally assumed to be constant across the brain, is a necessary step to obtain regional estimates of the specific fractions. The nondisplaceable binding can be directly measured if a reference region, i.e. a region devoid of any specific binding, is available. Many receptors are however widely expressed across the brain, and a true reference region is rarely available. In these cases, the nonspecific binding can be obtained after competitive pharmacological blockade, which is often contraindicated in humans. In this work we introduce the genomic plot for estimating the nondisplaceable fraction using baseline scans only. The genomic plot is a transformation of the Lassen graphical method in which the brain maps of mRNA transcripts of the target receptor obtained from the Allen brain atlas are used as a surrogate measure of the specific binding. Thus, the genomic plot allows the calculation of the specific and nondisplaceable components of radioligand uptake without the need of pharmacological blockade. We first assessed the statistical properties of the method with computer simulations. Then we sought ground-truth validation using human PET datasets of seven different neuroreceptor radioligands, where nonspecific fractions were either obtained separately using drug displacement or available from a true reference region. The population nondisplaceable fractions estimated by the genomic plot were very close to those measured by actual human blocking studies (mean relative difference between 2% and 7%). However, these estimates were valid only when mRNA expressions were predictive of protein levels (i

  2. Measuring specific receptor binding of a PET radioligand in human brain without pharmacological blockade: The genomic plot.

    PubMed

    Veronese, Mattia; Zanotti-Fregonara, Paolo; Rizzo, Gaia; Bertoldo, Alessandra; Innis, Robert B; Turkheimer, Federico E

    2016-04-15

    PET studies allow in vivo imaging of the density of brain receptor species. The PET signal, however, is the sum of the fraction of radioligand that is specifically bound to the target receptor and the non-displaceable fraction (i.e. the non-specifically bound radioligand plus the free ligand in tissue). Therefore, measuring the non-displaceable fraction, which is generally assumed to be constant across the brain, is a necessary step to obtain regional estimates of the specific fractions. The nondisplaceable binding can be directly measured if a reference region, i.e. a region devoid of any specific binding, is available. Many receptors are however widely expressed across the brain, and a true reference region is rarely available. In these cases, the nonspecific binding can be obtained after competitive pharmacological blockade, which is often contraindicated in humans. In this work we introduce the genomic plot for estimating the nondisplaceable fraction using baseline scans only. The genomic plot is a transformation of the Lassen graphical method in which the brain maps of mRNA transcripts of the target receptor obtained from the Allen brain atlas are used as a surrogate measure of the specific binding. Thus, the genomic plot allows the calculation of the specific and nondisplaceable components of radioligand uptake without the need of pharmacological blockade. We first assessed the statistical properties of the method with computer simulations. Then we sought ground-truth validation using human PET datasets of seven different neuroreceptor radioligands, where nonspecific fractions were either obtained separately using drug displacement or available from a true reference region. The population nondisplaceable fractions estimated by the genomic plot were very close to those measured by actual human blocking studies (mean relative difference between 2% and 7%). However, these estimates were valid only when mRNA expressions were predictive of protein levels (i

  3. Distributed analysis in ATLAS

    NASA Astrophysics Data System (ADS)

    Dewhurst, A.; Legger, F.

    2015-12-01

    The ATLAS experiment accumulated more than 140 PB of data during the first run of the Large Hadron Collider (LHC) at CERN. The analysis of such an amount of data is a challenging task for the distributed physics community. The Distributed Analysis (DA) system of the ATLAS experiment is an established and stable component of the ATLAS distributed computing operations. About half a million user jobs are running daily on DA resources, submitted by more than 1500 ATLAS physicists. The reliability of the DA system during the first run of the LHC and the following shutdown period has been high thanks to the continuous automatic validation of the distributed analysis sites and the user support provided by a dedicated team of expert shifters. During the LHC shutdown, the ATLAS computing model has undergone several changes to improve the analysis workflows, including the re-design of the production system, a new analysis data format and event model, and the development of common reduction and analysis frameworks. We report on the impact such changes have on the DA infrastructure, describe the new DA components, and include recent performance measurements.

  4. Automatic brain segmentation in rhesus monkeys

    NASA Astrophysics Data System (ADS)

    Styner, Martin; Knickmeyer, Rebecca; Joshi, Sarang; Coe, Christopher; Short, Sarah J.; Gilmore, John

    2007-03-01

    Many neuroimaging studies are applied to primates as pathologies and environmental exposures can be studied in well-controlled settings and environment. In this work, we present a framework for both the semi-automatic creation of a rhesus monkey atlas and a fully automatic segmentation of brain tissue and lobar parcellation. We determine the atlas from training images by iterative, joint deformable registration into an unbiased average image. On this atlas, probabilistic tissue maps and a lobar parcellation. The atlas is then applied via affine, followed by deformable registration. The affinely transformed atlas is employed for a joint T1/T2 based tissue classification. The deformed atlas parcellation masks the tissue segmentations to define the parcellation. Other regional definitions on the atlas can also straightforwardly be used as segmentation. We successfully built average atlas images for the T1 and T2 datasets using a developmental training datasets of 18 cases aged 16-34 months. The atlas clearly exhibits an enhanced signal-to-noise ratio compared to the original images. The results further show that the cortical folding variability in our data is highly limited. Our segmentation and parcellation procedure was successfully re-applied to all training images, as well as applied to over 100 additional images. The deformable registration was able to identify corresponding cortical sulcal borders accurately. Even though the individual methods used in this segmentation framework have been applied before on human data, their combination is novel, as is their adaptation and application to rhesus monkey MRI data. The reduced variability present in the primate data results in a segmentation pipeline that exhibits high stability and anatomical accuracy.

  5. Evaluation of effects of groundwater withdrawals at the proposed Allen combined-cycle combustion turbine plant, Shelby County, Tennessee

    USGS Publications Warehouse

    Haugh, Connor J.

    2016-01-01

    The Mississippi Embayment Regional Aquifer Study groundwater-flow model was used to simulate the potential effects of future groundwater withdrawals at the proposed Allen combined-cycle combustion turbine plant in Shelby County, Tennessee. The scenario used in the simulation consisted of a 30-year average withdrawal period followed by a 30-day maximum withdrawal period. Effects of withdrawals at the Allen plant site on the Mississippi embayment aquifer system were evaluated by comparing the difference in simulated water levels in the aquifers at the end of the 30-year average withdrawal period and at the end of the scenario to a base case without the Allen combined-cycle combustion turbine plant withdrawals. Simulated potentiometric surface declines in the Memphis aquifer at the Allen plant site were about 7 feet at the end of the 30-year average withdrawal period and 11 feet at the end of the scenario. The affected area of the Memphis aquifer at the Allen plant site as delineated by the 4-foot potentiometric surface-decline contour was 2,590 acres at the end of the 30-year average withdrawal period and 11,380 acres at the end of the scenario. Simulated declines in the underlying Fort Pillow aquifer and overlying shallow aquifer were both less than 1 foot at the end of the 30-year average withdrawal period and the end of the scenario.

  6. Science Highlights from the RBSP-ECT Particle Instrument Suite on NASA's Van Allen Probes Mission

    NASA Astrophysics Data System (ADS)

    Spence, Harlan

    2014-05-01

    The NASA Van Allen Probes mission includes an instrument suite known as the Radiation Belt Storm Probes (RBSP) - Energetic Particle, Composition, and Thermal Plasma (ECT) suite. RBSP-ECT contains a well-proven complement of particle instruments to ensure the highest quality measurements ever made in the radiation belts and the inner magnetosphere. The coordinated RBSP-ECT particle measurements, analyzed in combination with fields and waves observations and state of-the-art theory and modeling, provide new understanding on the acceleration, global distribution, and variability of radiation belt electrons and ions, key science objectives of NASA's Living With a Star program and the Van Allen Probes mission. The RBSP-ECT suite consists of three highly-coordinated instruments: the Helium Oxygen Proton Electron (HOPE) spectrometer, the Magnetic Electron Ion Spectrometer (MagEIS), and the Relativistic Electron Proton Telescope (REPT). Collectively these three instrument types cover comprehensively the full electron and ion spectra from one eV to 10's of MeV with sufficient energy resolution, pitch angle coverage and resolution, and with composition measurements in the critical energy range up to 50 keV and also from a few to 50 MeV/nucleon. All three instruments are based on measurement techniques proven in the radiation belts, then optimized to provide unambiguous separation of ions and electrons and clean energy responses even in the presence of extreme penetrating background environments. In this presentation, we summarize overall ECT science goals and then show scientific results derived from the ECT suite on the dual Van Allen Probes spacecraft to date. Mission operations began only in late October 2012, and we have now achieved significant results. Results presented here will include substantial progress toward resolving primary Van Allen Probes science targets, such as: the relative role of localized acceleration versus transport-generated particle acceleration

  7. Engaging Allene-Derived Zwitterions in an Unprecedented Mode of Asymmetric [3+2]-Annulation Reaction.

    PubMed

    Sankar, Muthukumar G; Garcia-Castro, Miguel; Golz, Christopher; Strohmann, Carsten; Kumar, Kamal

    2016-08-01

    Catalytic addition of chiral phosphine, that is, (R)- or (S)-SITCP, to an α-substituted allene ester generated a zwitterionic dipole. Under optimized reaction conditions, this dipole could engage isatine-derived N-Boc-ketimines in a novel mode of [3+2] annulation reaction. Pyrrolinyl spirooxindoles are thus afforded in high yields and with excellent enantioselectivities. The unprecedented annulation reaction successfully facilitated the construction of sp(3) -rich and highly substituted 3,2'-pyrrolidinyl spirooxindoles supporting many chiral centers. PMID:27345724

  8. MEDICAL MANAGEMENT OF LEIOMYOMATA AND SUSPECTED ENDOMETRIOSIS IN AN ALLEN'S SWAMP MONKEY (ALLENOPITHECUS NIGROVIRIDUS).

    PubMed

    Jafarey, Yousuf S; Hanley, Christopher S; Berlinski, Ric A; Warner, Connie; Armstrong, Anthony

    2015-12-01

    A 13-yr-old female nulliparous Allen's swamp monkey (Allenopitchecus nigroviridis) presented with intermittent excessive vaginal bleeding, cyclical lethargy, and a history of irregular menstrual cycles. Abdominal ultrasonography revealed a subjectively thickened, irregular endometrium, multiple leiomyomata (uterine fibroids), and bilateral anechoic foci on the ovaries. Treatment was initiated with leuprolide acetate i.m. monthly for 6 mo. Recheck ultrasound at 3 mo showed a decrease in leiomyoma diameter and no evidence of active follicles on the ovaries. Eleven months following completion of treatment, clinical signs recurred and the animal was treated with a deslorelin implant. Since implant placement, no vaginal bleeding has been noted. PMID:26667550

  9. Allenes as three-carbon units in catalytic cycloadditions: new opportunities with transition-metal catalysts.

    PubMed

    López, Fernando; Mascareñas, José Luis

    2011-01-10

    Allenes are very versatile synthetic units that are used in many types of catalytic cycloaddition reactions. Most examples reported so far involve their use as 2C-atom components, whereas their participations as 3C-atom components have been much less frequent. In this concept article, we present an overview of this latter strategy, emphasizing on those more recent contributions involving the use of Pt(II) and Au(I) catalysts, which have uncovered new opportunities in this area. PMID:21207554

  10. Kinetics of the acid-catalyzed hydration of allene and propyne

    SciTech Connect

    Cramer, P.; Tidwell, T.T.

    1981-06-19

    The kinetics of the conversion of allene and propyne to acetone in aqueous sulfuric acid have been measured. The solvent isotope effects k/sub H/sup +//k/sub D/sup +// and the dependence of the rates on acidity are consistent with the Ad/sub E/2 mechanism of rate-limiting protonation at the terminal carbons leading to the intermediate 2-propenyl cation CH/sub 3/C/sup +/H=CH/sub 2/ in each case, followed by hydration to the enol and isomerization to acetone. This route is strongly favored by published theoretical studies. (2 tables)

  11. Shielding of manned space stations against Van Allen Belt protons: a preliminary scoping study

    SciTech Connect

    Santoro, R.T.; Alsmiller, R.G. Jr.; Barnes, J.M.; Corbin, J.M.

    1986-09-01

    Calculated results are presented to aid in the design of the shielding required to protect astronauts in a space station that is orbiting through the Van Allen proton belt. The geometry considered - a spherical shell shield with a spherical tissue phantom at its center - is only a very approximate representation of an actual space station, but this simple geometry makes it possible to consider a wide range of possible shield materials. Both homogeneous and laminated shields are considered. Also, an approximation procedure - the equivalent thickness approximation - that allows dose rates to be estimated for any shield material or materials from the dose rates for an aluminum shield is presented and discussed.

  12. The Allen Telescope Array: The First Widefield, Panchromatic, Snapshot Radio Camera for Radio Astronomy and SETI

    NASA Astrophysics Data System (ADS)

    Welch, J.; Backer, D.; Blitz, L.; Bock, D. C.-J.; Bower, G. C.; Cheng, C.; Croft, S.; Dexter, M.; Engargiola, G.; Fields, E.; Forster, J.; Gutierrez-Kraybill, C.; Heiles, C.; Helfer, T.; Jorgensen, S.; Keating, G.; Lugten, J.; MacMahon, D.; Milgrome, O.; Thornton, D.; Urry, L.; van Leeuwen, J.; Werthimer, D.; Williams, P. H.; Wright, M.; Tarter, J.; Ackermann, R.; Atkinson, S.; Backus, P.; Barott, W.; Bradford, T.; Davis, M.; Deboer, D.; Dreher, J.; Harp, G.; Jordan, J.; Kilsdonk, T.; Pierson, T.; Randall, K.; Ross, J.; Shostak, S.; Fleming, M.; Cork, C.; Vitouchkine, A.; Wadefalk, N.; Weinreb, S.

    2009-08-01

    The first 42 elements of the Allen Telescope Array (ATA-42) are beginning to deliver data at the Hat Creek Radio Observatory in Northern California. Scientists and engineers are actively exploiting all of the flexibility designed into this innovative instrument for simultaneously conducting surveys of the astrophysical sky and conducting searches for distant technological civilizations. This paper summarizes the design elements of the ATA, the cost savings made possible by the use of COTS components, and the cost/performance trades that eventually enabled this first snapshot radio camera. The fundamental scientific program of this new telescope is varied and exciting; some of the first astronomical results will be discussed.

  13. Construction of 4D high-definition cortical surface atlases of infants: Methods and applications.

    PubMed

    Li, Gang; Wang, Li; Shi, Feng; Gilmore, John H; Lin, Weili; Shen, Dinggang

    2015-10-01

    In neuroimaging, cortical surface atlases play a fundamental role for spatial normalization, analysis, visualization, and comparison of results across individuals and different studies. However, existing cortical surface atlases created for adults are not suitable for infant brains during the first two postnatal years, which is the most dynamic period of postnatal structural and functional development of the highly-folded cerebral cortex. Therefore, spatiotemporal cortical surface atlases for infant brains are highly desired yet still lacking for accurate mapping of early dynamic brain development. To bridge this significant gap, leveraging our infant-dedicated computational pipeline for cortical surface-based analysis and the unique longitudinal infant MRI dataset acquired in our research center, in this paper, we construct the first spatiotemporal (4D) high-definition cortical surface atlases for the dynamic developing infant cortical structures at seven time points, including 1, 3, 6, 9, 12, 18, and 24 months of age, based on 202 serial MRI scans from 35 healthy infants. For this purpose, we develop a novel method to ensure the longitudinal consistency and unbiasedness to any specific subject and age in our 4D infant cortical surface atlases. Specifically, we first compute the within-subject mean cortical folding by unbiased groupwise registration of longitudinal cortical surfaces of each infant. Then we establish longitudinally-consistent and unbiased inter-subject cortical correspondences by groupwise registration of the geometric features of within-subject mean cortical folding across all infants. Our 4D surface atlases capture both longitudinally-consistent dynamic mean shape changes and the individual variability of cortical folding during early brain development. Experimental results on two independent infant MRI datasets show that using our 4D infant cortical surface atlases as templates leads to significantly improved accuracy for spatial normalization

  14. Atlas Regeneration, Inc.

    PubMed

    Makarev, Eugene; Isayev, Olexandr; Atala, Anthony

    2016-03-01

    Atlas Regeneration is dedicated to the development of novel data-driven solutions for regenerative medicine, adapting proven technologies, and analysis strategies to take a multiomics-wide view of stem cell quality and cell fate design. Our core offering is a global comprehensive map of stem cell differentiation, Universal Signalome Atlas for Regenerative Medicine, reflecting the pathway activation states across all characterized stem cells and their differentiated products. Key applications of Universal Signalome Atlas for Regenerative Medicine will include quality assurance for engineered cell products, and directed regeneration pharmacology, where we will screen and identify compounds that can efficiently convert pluripotent cells into desired subtypes. Another marketable piece of IP is development of specialized signaling pathway analysis systems Regeneration Intelligence which supposed to target the unmet needs of determination and prediction of stem cell signaling pathway activation to govern cell differentiation in specific directions. PMID:26925598

  15. Calorimetry Triggering in ATLAS

    SciTech Connect

    Igonkina, O.; Achenbach, R.; Adragna, P.; Aharrouche, M.; Alexandre, G.; Andrei, V.; Anduaga, X.; Aracena, I.; Backlund, S.; Baines, J.; Barnett, B.M.; Bauss, B.; Bee, C.; Behera, P.; Bell, P.; Bendel, M.; Benslama, K.; Berry, T.; Bogaerts, A.; Bohm, C.; Bold, T.; /UC, Irvine /AGH-UST, Cracow /Birmingham U. /Barcelona, IFAE /CERN /Birmingham U. /Rutherford /Montreal U. /Santa Maria U., Valparaiso /DESY /DESY, Zeuthen /Geneva U. /City Coll., N.Y. /Barcelona, IFAE /CERN /Birmingham U. /Kirchhoff Inst. Phys. /Birmingham U. /Lisbon, LIFEP /Rio de Janeiro Federal U. /City Coll., N.Y. /Birmingham U. /Copenhagen U. /Copenhagen U. /Brookhaven /Rutherford /Royal Holloway, U. of London /Pennsylvania U. /Montreal U. /SLAC /CERN /Michigan State U. /Chile U., Catolica /City Coll., N.Y. /Oxford U. /La Plata U. /McGill U. /Mainz U., Inst. Phys. /Hamburg U. /DESY /DESY, Zeuthen /Geneva U. /Queen Mary, U. of London /CERN /Rutherford /Rio de Janeiro Federal U. /Birmingham U. /Montreal U. /CERN /Kirchhoff Inst. Phys. /Liverpool U. /Royal Holloway, U. of London /Pennsylvania U. /Kirchhoff Inst. Phys. /Geneva U. /Birmingham U. /NIKHEF, Amsterdam /Rutherford /Royal Holloway, U. of London /Rutherford /Royal Holloway, U. of London /AGH-UST, Cracow /Mainz U., Inst. Phys. /Mainz U., Inst. Phys. /Birmingham U. /Hamburg U. /DESY /DESY, Zeuthen /Geneva U. /Kirchhoff Inst. Phys. /Michigan State U. /Stockholm U. /Stockholm U. /Birmingham U. /CERN /Montreal U. /Stockholm U. /Arizona U. /Regina U. /Regina U. /Rutherford /NIKHEF, Amsterdam /Kirchhoff Inst. Phys. /DESY /DESY, Zeuthen /City Coll., N.Y. /University Coll. London /Humboldt U., Berlin /Queen Mary, U. of London /Argonne /LPSC, Grenoble /Arizona U. /Kirchhoff Inst. Phys. /Birmingham U. /Antonio Narino U. /Hamburg U. /DESY /DESY, Zeuthen /Kirchhoff Inst. Phys. /Birmingham U. /Chile U., Catolica /Indiana U. /Manchester U. /Kirchhoff Inst. Phys. /Rutherford /City Coll., N.Y. /Stockholm U. /La Plata U. /Antonio Narino U. /Queen Mary, U. of London /Kirchhoff Inst. Phys. /Antonio Narino U. /Pavia U. /City Coll., N.Y. /Mainz U., Inst. Phys. /Mainz U., Inst. Phys. /Pennsylvania U. /Barcelona, IFAE /Barcelona, IFAE /Chile U., Catolica /Genoa U. /INFN, Genoa /Rutherford /Barcelona, IFAE /Nevis Labs, Columbia U. /CERN /Antonio Narino U. /McGill U. /Rutherford /Santa Maria U., Valparaiso /Rutherford /Chile U., Catolica /Brookhaven /Oregon U. /Mainz U., Inst. Phys. /Barcelona, IFAE /McGill U. /Antonio Narino U. /Antonio Narino U. /Kirchhoff Inst. Phys. /Sydney U. /Rutherford /McGill U. /McGill U. /Pavia U. /Genoa U. /INFN, Genoa /Kirchhoff Inst. Phys. /Kirchhoff Inst. Phys. /Mainz U., Inst. Phys. /Barcelona, IFAE /SLAC /Stockholm U. /Moscow State U. /Stockholm U. /Birmingham U. /Kirchhoff Inst. Phys. /DESY /DESY, Zeuthen /Birmingham U. /Geneva U. /Oregon U. /Barcelona, IFAE /University Coll. London /Royal Holloway, U. of London /Birmingham U. /Mainz U., Inst. Phys. /Birmingham U. /Birmingham U. /Oregon U. /La Plata U. /Geneva U. /Chile U., Catolica /McGill U. /Pavia U. /Barcelona, IFAE /Regina U. /Birmingham U. /Birmingham U. /Kirchhoff Inst. Phys. /Oxford U. /CERN /Kirchhoff Inst. Phys. /UC, Irvine /UC, Irvine /Wisconsin U., Madison /Rutherford /Mainz U., Inst. Phys. /CERN /Geneva U. /Copenhagen U. /City Coll., N.Y. /Wisconsin U., Madison /Rio de Janeiro Federal U. /Wisconsin U., Madison /Stockholm U. /University Coll. London

    2011-12-08

    The ATLAS experiment is preparing for data taking at 14 TeV collision energy. A rich discovery physics program is being prepared in addition to the detailed study of Standard Model processes which will be produced in abundance. The ATLAS multi-level trigger system is designed to accept one event in 2/10{sup 5} to enable the selection of rare and unusual physics events. The ATLAS calorimeter system is a precise instrument, which includes liquid Argon electro-magnetic and hadronic components as well as a scintillator-tile hadronic calorimeter. All these components are used in the various levels of the trigger system. A wide physics coverage is ensured by inclusively selecting events with candidate electrons, photons, taus, jets or those with large missing transverse energy. The commissioning of the trigger system is being performed with cosmic ray events and by replaying simulated Monte Carlo events through the trigger and data acquisition system.

  16. Spatially adapted augmentation of age-specific atlas-based segmentation using patch-based priors

    NASA Astrophysics Data System (ADS)

    Liu, Mengyuan; Seshamani, Sharmishtaa; Harrylock, Lisa; Kitsch, Averi; Miller, Steven; Chau, Van; Poskitt, Kenneth; Rousseau, Francois; Studholme, Colin

    2014-03-01

    One of the most common approaches to MRI brain tissue segmentation is to employ an atlas prior to initialize an Expectation- Maximization (EM) image labeling scheme using a statistical model of MRI intensities. This prior is commonly derived from a set of manually segmented training data from the population of interest. However, in cases where subject anatomy varies significantly from the prior anatomical average model (for example in the case where extreme developmental abnormalities or brain injuries occur), the prior tissue map does not provide adequate information about the observed MRI intensities to ensure the EM algorithm converges to an anatomically accurate labeling of the MRI. In this paper, we present a novel approach for automatic segmentation of such cases. This approach augments the atlas-based EM segmentation by exploring methods to build a hybrid tissue segmentation scheme that seeks to learn where an atlas prior fails (due to inadequate representation of anatomical variation in the statistical atlas) and utilize an alternative prior derived from a patch driven search of the atlas data. We describe a framework for incorporating this patch-based augmentation of EM (PBAEM) into a 4D age-specific atlas-based segmentation of developing brain anatomy. The proposed approach was evaluated on a set of MRI brain scans of premature neonates with ages ranging from 27.29 to 46.43 gestational weeks (GWs). Results indicated superior performance compared to the conventional atlas-based segmentation method, providing improved segmentation accuracy for gray matter, white matter, ventricles and sulcal CSF regions.

  17. Magnetic resonance imaging of the pediatric brain

    SciTech Connect

    Salamon, G.; Raynaud, C.; Regis, J.; Rumeau, C.

    1990-01-01

    The atlas presents sequences of MRI sections parallel to the orbito-meatal plane in children from birth through the age of sixteen years. Each child was studied horizontally and sagitally and three-dimensional brain images were reconstructed to facilitate accurate identification of sulci and gyri. The images show crucial aspects of brain development such as the constancy of the brain stem and primitive brain from birth onward; the development of the telencephalon, characterized by deepening of sulci and growth of the cerebral cortex surface; and the different stages of white matter myelinization.

  18. The Herschel ATLAS

    NASA Technical Reports Server (NTRS)

    Eales, S.; Dunne, L.; Clements, D.; Cooray, A.; De Zotti, G.; Dye, S.; Ivison, R.; Jarvis, M.; Lagache, G.; Maddox, S.; Negrello, M.; Serjeant, S.; Thompson, M. A.; Van Kampen, E.; Amblard, A.; Andreani, P.; Baes, M.; Beelen, A.; Bendo, G. J.; Bertoldi, F.; Benford, D.; Bock, J.

    2010-01-01

    The Herschel ATLAS is the largest open-time key project that will be carried out on the Herschel Space Observatory. It will survey 570 sq deg of the extragalactic sky, 4 times larger than all the other Herschel extragalactic surveys combined, in five far-infrared and submillimeter bands. We describe the survey, the complementary multiwavelength data sets that will be combined with the Herschel data, and the six major science programs we are undertaking. Using new models based on a previous submillimeter survey of galaxies, we present predictions of the properties of the ATLAS sources in other wave bands.

  19. Internet-enabled high-resolution brain mapping and virtual microscopy.

    PubMed

    Mikula, Shawn; Trotts, Issac; Stone, James M; Jones, Edward G

    2007-03-01

    Virtual microscopy involves the conversion of histological sections mounted on glass microscope slides to high-resolution digital images. Virtual microscopy offers several advantages over traditional microscopy, including remote viewing and data sharing, annotation, and various forms of data mining. We describe a method utilizing virtual microscopy for generation of internet-enabled, high-resolution brain maps and atlases. Virtual microscopy-based digital brain atlases have resolutions approaching 100,000 dpi, which exceeds by three or more orders of magnitude resolutions obtainable in conventional print atlases, MRI, and flat-bed scanning. Virtual microscopy-based digital brain atlases are superior to conventional print atlases in five respects: (1) resolution, (2) annotation, (3) interaction, (4) data integration, and (5) data mining. Implementation of virtual microscopy-based digital brain atlases is located at BrainMaps.org, which is based on more than 10 million megapixels (35 terabytes) of scanned images of serial sections of primate and non-primate brains with a resolution of 0.46 microm/pixel (55,000 dpi). The method can be replicated by labs seeking to increase accessibility and sharing of neuroanatomical data. Online tools offer the possibility of visualizing and exploring completely digitized sections of brains at a sub-neuronal level and can facilitate large-scale connectional tracing, histochemical, and stereological analyses. PMID:17229579

  20. Mapping genetic influences on human brain structure.

    PubMed

    Thompson, Paul; Cannon, Tyrone D; Toga, Arthur W

    2002-01-01

    Recent advances in brain imaging and genetics have empowered the mapping of genetic and environmental influences on the human brain. These techniques shed light on the 'nature/nurture' debate, revealing how genes determine individual differences in intelligence quotient (IQ) or risk for disease. They visualize which aspects of brain structure and function are heritable, and to what degree, linking these features with behavioral or cognitive traits or disease phenotypes. In genetically transmitted disorders such as schizophrenia, patterns of brain structure can be associated with increased disease liability, and sites can be mapped where non-genetic triggers may initiate disease. We recently developed a large-scale computational brain atlas, including data components from the Finnish Twin registry, to store information on individual variations in brain structure and their heritability. Algorithms from random field theory, anatomical modeling, and population genetics were combined to detect a genetic continuum in which brain structure is heavily genetically determined in some areas but not others. These algorithmic advances motivate studies of disease in which the normative atlas acts as a quantitative reference for the heritability of structural differences and deficits in patient populations. The resulting genetic brain maps isolate biological markers for inherited traits and disease susceptibility, which may serve as targets for genetic linkage and association studies. Computational methods from brain imaging and genetics can be fruitfully merged, to shed light on the inheritance of personality differences and behavioral traits, and the genetic transmission of diseases that affect the human brain. PMID:12553492

  1. Chiroptical properties and the racemization of pyrene and tetrathiafulvalene-substituted allene: substitution and solvent effects on racemization in tetrathiafulvalenylallene.

    PubMed

    Hasegawa, Masashi; Iwata, Seiya; Sone, Yasuto; Endo, Junta; Matsuzawa, Hideyo; Mazaki, Yasuhiro

    2014-01-01

    Dissymmetric 1,3-diphenylallene derivative 3 connected with 4,5-bis(methyl-thio)tetrathiafulvalenyl and 1-pyrenyl substituents was prepared and characterized. The molecular structure was determined by X-ray crystallographic analysis. Optical resolution was accomplished using a recycling chiral HPLC, and its chiroptical properties were examined with optical rotation and electronic circular dichroism (ECD) spectra. The title compound underwent photoracemization under daylight. This behavior was investigated in various solvents and compared with that of 1,3-bis(tetrathiafulvalenyl)allene (bis-TTF-allene) derivative 2. The first-order rate plot of the intensity of the ECD spectra at a given time interval gave the rate of racemization. Mild racemization was observed in polar solvents, whereas a relatively fast rate was obtained in less polar solvents. In addition, the TTF groups of the allene also accelerate the racemization rate. These results suggest that the racemization mechanism occurs via a non-polar diradical structure. PMID:24599123

  2. An impenetrable barrier to ultrarelativistic electrons in the Van Allen radiation belts.

    PubMed

    Baker, D N; Jaynes, A N; Hoxie, V C; Thorne, R M; Foster, J C; Li, X; Fennell, J F; Wygant, J R; Kanekal, S G; Erickson, P J; Kurth, W; Li, W; Ma, Q; Schiller, Q; Blum, L; Malaspina, D M; Gerrard, A; Lanzerotti, L J

    2014-11-27

    Early observations indicated that the Earth's Van Allen radiation belts could be separated into an inner zone dominated by high-energy protons and an outer zone dominated by high-energy electrons. Subsequent studies showed that electrons of moderate energy (less than about one megaelectronvolt) often populate both zones, with a deep 'slot' region largely devoid of particles between them. There is a region of dense cold plasma around the Earth known as the plasmasphere, the outer boundary of which is called the plasmapause. The two-belt radiation structure was explained as arising from strong electron interactions with plasmaspheric hiss just inside the plasmapause boundary, with the inner edge of the outer radiation zone corresponding to the minimum plasmapause location. Recent observations have revealed unexpected radiation belt morphology, especially at ultrarelativistic kinetic energies (more than five megaelectronvolts). Here we analyse an extended data set that reveals an exceedingly sharp inner boundary for the ultrarelativistic electrons. Additional, concurrently measured data reveal that this barrier to inward electron radial transport does not arise because of a physical boundary within the Earth's intrinsic magnetic field, and that inward radial diffusion is unlikely to be inhibited by scattering by electromagnetic transmitter wave fields. Rather, we suggest that exceptionally slow natural inward radial diffusion combined with weak, but persistent, wave-particle pitch angle scattering deep inside the Earth's plasmasphere can combine to create an almost impenetrable barrier through which the most energetic Van Allen belt electrons cannot migrate. PMID:25428500

  3. Observations and Simulations of Whistler-mode Waves Detected by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Bengtson, M.; Rosborough, S.; Stein, R. L.; Streltsov, A. V.; Matheny, M. M.

    2015-12-01

    In March of 2014, Van Allen Probe A observed several packets of whistler-mode waves while passing through the apogee of an orbit on the dayside magnetosphere. These waves were localized in regions of strong density inhomogeneity. For one observed wave, the wave maximum occurred within the center of the channel formed by a density enhancement. The other two waves were observed on either side of strong density depletion. We first determine the wave characteristics using data from Van Allen Probe A. Then, we use the observations to specify parameters in an electron MHD simulation to model the propagation of whistler-mode waves inside density structures. These observations and simulations demonstrate how whistler-mode waves can become trapped inside density structures, a phenomenon known as ducting. The density ducts serve to guide the whistler-mode waves into the earth's radiation belt while minimizing damping effects. The purpose of this research is to understand the role of density ducts in guiding whistler-mode waves, which will have important applications for remediation of energetic particles from the radiation belt.

  4. Purification and Characterization of Allene Oxide Cyclase from Dry Corn Seeds.

    PubMed Central

    Ziegler, J.; Hamberg, M.; Miersch, O.; Parthier, B.

    1997-01-01

    Allene oxide cyclase (AOC; EC 5.3.99.6) catalyzes the cyclization of 12,13(S)-epoxy-9(Z),11,15(Z)-octadecatrienoic acid to 12-oxo- 10,15(Z)-phytodienoic acid, the precursor of jasmonic acid (JA). This soluble enzyme was purified 2000-fold from dry corn (Zea mays L.) kernels to apparent homogeneity. The dimeric protein has a molecular mass of 47 kD. Allene oxide cyclase activity was not affected by divalent ions and was not feedback-regulated by its product, 12-oxo-l0,15(Z)-phytodienoic acid, or by JA. ([plus or minus])-cis- 12,13-Epoxy-9(Z)-octadecenoic acid, a substrate analog, strongly inhibited the enzyme, with 50% inhibition at 20 [mu]M. Modification of the inhibitor, such as methylation of the carboxyl group or a shift in the position of the epoxy group, abolished the inhibitory effect, indicating that both structural elements and their position are essential for binding to AOC. Nonsteroidal anti-inflammatory drugs, which are often used to interfere with JA biosynthesis, did not influence AOC activity. The purified enzyme catalyzed the cyclization of 12,13(S)-epoxy-9(Z),11,15(Z)-octadecatrienoic acid derived from linolenic acid, but not that of 12,13(S)-epoxy-9(Z),11- octadecadienoic acid derived from linoleic acid. PMID:12223729

  5. 'Trunk-like' ion structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Kistler, L. M.; Spence, H.; Wolf, R.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.; Larsen, B.; Niehof, J. T.; MacDonald, E.; Friedel, R. H.

    2013-12-01

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. In this study, we report 'trunk-like' ion structures observed in situ by the Van Allen Probes on 2 November 2012. The trunk structures are present in heavy ions but not in H+. For the particular event, ion energies in the He+ trunks, located at L = 3.7-2.6, MLT = 8.8-10.3, and MLAT = -2.0-0.03°, vary monotonically from 3.5 to 0.04 keV. It is suggested that the trunk phenomenon is due to a combination of 1) deeper ion injections from storm activity, 2) the longer charge exchange lifetimes of heavy ions than H+, 3) the separation of a narrow layer of ions around the Alfvén layer from other convecting ions, and 4) the trajectory of the Van Allen Probes (i.e., an orbital effect). Both observation analysis and numerical modeling are utilized in the study.

  6. A molecular dynamics examination on mutation-induced catalase activity in coral allene oxide synthase.

    PubMed

    De Luna, Phil; Bushnell, Eric A C; Gauld, James W

    2013-11-27

    Coral allene oxide synthase (cAOS) catalyzes the formation of allene oxides from fatty acid hydroperoxides. Interestingly, its active site differs from that of catalase by only a single residue yet is incapable of catalase activity. That is, it is unable to catalyze the decomposition of hydrogen peroxide to molecular oxygen and water. However, the single active-site mutation T66V allows cAOS to exhibit catalase activity. We have performed a series of molecular dynamics (MD) simulations in order to gain insights into the differences in substrate (8R-hydroperoxyeicosatetraenoic) and H2O2 active site binding between wild-type cAOS and the T66V mutant cAOS. It is observed that in wild-type cAOS the active site Thr66 residue consistently forms a strong hydrogen-bonding interaction with H2O2 (catalase substrate) and, importantly, with the aid of His67 helps to pull H2O2 away from the heme Fe center. In contrast, in the T66V-cAOS mutant the H2O2 is much closer to the heme's Fe center and now forms a consistent Fe···O2H2 interaction. In addition, the His67···H2O2 distance shortens considerably, increasing the likelihood of a Cpd I intermediate and hence exhibiting catalase activity. PMID:24164352

  7. Ultrarelativistic electrons in the Van Allen belts: RPS observations and Geant4 simulations

    NASA Astrophysics Data System (ADS)

    Looper, M. D.; Mazur, J. E.; O'Brien, T. P., III; Blake, J. B.; George, J. S.

    2015-12-01

    The Relativistic Proton Spectrometer (RPS) aboard the Van Allen Probes spacecraft is designed to measure protons from about 60 MeV to multiple GeV, but it is also sensitive to electrons above several MeV. Its Cherenkov subsystem provides energy resolution for protons above a few hundred MeV, and electrons at extremely high energies, around 50 MeV and above, can also produce high levels of Cherenkov light. While mapping protons in the inner Van Allen Belt with RPS, Mazur et al. (Fall 2014 AGU meeting, paper SM22A-02) observed a concentration of particle events around L = 2 with Cherenkov light corresponding to protons at energies well above the limit for stable trapping there. We present a preliminary analysis that shows that the patterns of the Cherenkov light distribution are consistent with these particle events instead being caused by electrons at energies of at least several tens of MeV. This energy range is well above that expected from magnetospheric energization, even by a violent event like the March 1991 shock, which injected electrons peaked around 15 MeV (Looper et al., GRL 1994, doi:10.1029/94GL01586). We discuss the possibility that these electrons are instead due to the decay of pions and muons produced by cosmic-ray interactions with the atmosphere, with a characteristic energy set by the pion rest mass of 140 MeV.

  8. Genetic diversity and structure in the Endangered Allen Cays Rock Iguana, Cyclura cychlura inornata

    PubMed Central

    Aplasca, Andrea C.; Iverson, John B.; Welch, Mark E.; Colosimo, Giuliano

    2016-01-01

    The Endangered Allen Cays Rock Iguana (Cyclura cychlura inornata) is endemic to the Allen Cays, a tiny cluster of islands in the Bahamas. Naturally occurring populations exist on only two cays (<4 ha each). However, populations of unknown origin were recently discovered on four additional cays. To investigate patterns of genetic variation among these populations, we analyzed nuclear and mitochondrial markers for 268 individuals. Analysis of three mitochondrial gene regions (2,328 bp) and data for eight nuclear microsatellite loci indicated low genetic diversity overall. Estimates of effective population sizes based on multilocus genotypes were also extremely low. Despite low diversity, significant population structuring and variation in genetic diversity measures were detected among cays. Genetic data confirm the source population for an experimentally translocated population while raising concerns regarding other, unauthorized, translocations. Reduced heterozygosity is consistent with a documented historical population decline due to overharvest. This study provides the first range-wide genetic analysis of this subspecies. We suggest strategies to maximize genetic diversity during ongoing recovery including additional translocations to establish assurance populations and additional protective measures for the two remaining natural populations. PMID:26989628

  9. Mechanistic Insight into the Copper-Catalyzed Regiodivergent Silacarboxylation of Allenes with CO2.

    PubMed

    Yuan, Ruming; Hu, Rong; Fu, Gang

    2016-08-01

    DFT calculations were performed to investigate the detailed reaction mechanisms in the copper-catalyzed regiodivergent silacarboxylation of allenes. According to our calculations, the catalysis would bifurcate at the allene silylcupration step, followed by CO2 insertion, eventually leading to the carboxylated vinylsilane or allylsilane products. The gaps between the two silylcupration barriers were predicted to be -2.3, -0.4, and 2.2 kcal mol(-1) when using (rac)-Me-DuPhos, dcpe, and PCy3 (+H2 O) as the ligands, which nicely accounted for the experimental vinylsilane/allylsilane ratios of 93:7, 50:50, and 15:85, respectively. By means of transition-state-energy decomposition, we found that the energy penalty of catalyst deformation into its transition-state geometry was the key factor in determining the direction of the reaction. The switchable regioselectivity by using different P ligands could be ascribed to structural changes of the Cu-Si and Cu-P bonds during the silylcupration process. PMID:27319319

  10. New global loss model of energetic and relativistic electrons based on Van Allen Probes measurements

    NASA Astrophysics Data System (ADS)

    Orlova, Ksenia; Shprits, Yuri; Spasojevic, Maria

    2016-02-01

    The Electric and Magnetic Field Instrument Suite and Integrated Science (EMFISIS) instrument on the Van Allen Probes provides a vast quantity of fully resolved wave measurements below L = 5.5, a critical region for radiation belt acceleration and loss. EMFISIS data show that plasmaspheric hiss waves can be observed at frequencies as low as 20 Hz and provide three-component magnetic field measurements that can be directly used for electron scattering calculations. Updated models of hiss properties based on statistical analysis of Van Allen Probes data were recently developed. We use these new models to compute and parameterize the lifetime of electrons as a function of kinetic energy, L shell, Kp index, and magnetic local time. We present a detailed analysis of the electron lifetime sensitivity to the model of the wave intensity and spectral distribution. We also compare the results with previous models of electron loss, which were based on single-component electric field measurements from the sweep frequency receiver on board the CRRES satellite.

  11. An impenetrable barrier to ultrarelativistic electrons in the Van Allen radiation belts

    NASA Astrophysics Data System (ADS)

    Baker, D. N.; Jaynes, A. N.; Hoxie, V. C.; Thorne, R. M.; Foster, J. C.; Li, X.; Fennell, J. F.; Wygant, J. R.; Kanekal, S. G.; Erickson, P. J.; Kurth, W.; Li, W.; Ma, Q.; Schiller, Q.; Blum, L.; Malaspina, D. M.; Gerrard, A.; Lanzerotti, L. J.

    2014-11-01

    Early observations indicated that the Earth's Van Allen radiation belts could be separated into an inner zone dominated by high-energy protons and an outer zone dominated by high-energy electrons. Subsequent studies showed that electrons of moderate energy (less than about one megaelectronvolt) often populate both zones, with a deep `slot' region largely devoid of particles between them. There is a region of dense cold plasma around the Earth known as the plasmasphere, the outer boundary of which is called the plasmapause. The two-belt radiation structure was explained as arising from strong electron interactions with plasmaspheric hiss just inside the plasmapause boundary, with the inner edge of the outer radiation zone corresponding to the minimum plasmapause location. Recent observations have revealed unexpected radiation belt morphology, especially at ultrarelativistic kinetic energies (more than five megaelectronvolts). Here we analyse an extended data set that reveals an exceedingly sharp inner boundary for the ultrarelativistic electrons. Additional, concurrently measured data reveal that this barrier to inward electron radial transport does not arise because of a physical boundary within the Earth's intrinsic magnetic field, and that inward radial diffusion is unlikely to be inhibited by scattering by electromagnetic transmitter wave fields. Rather, we suggest that exceptionally slow natural inward radial diffusion combined with weak, but persistent, wave-particle pitch angle scattering deep inside the Earth's plasmasphere can combine to create an almost impenetrable barrier through which the most energetic Van Allen belt electrons cannot migrate.

  12. Impacts of intense inward and outward ULF wave radial diffusion on the Van Allen belts

    NASA Astrophysics Data System (ADS)

    Mann, Ian; Ozeke, Louis; Rae, I. Jonathan; Murphy, Kyle

    2016-07-01

    During geomagnetic storms, the power in ultra-low frequency (ULF) waves can be orders of magnitude larger than that predicted by statistics determined from an entire solar cycle. This is especially true during the main phase and early recovery phase. These periods of enhanced storm-time ULF wave power can have significant impacts on the morphology and structure of the Van Allen belts. Either fast inward or outward radial diffusion can result, depending on the profiles of the electron phase space density and the outer boundary condition at the edge of the belts. Small changes in the time sequence of powerful ULF waves, and the time sequence of any magnetopause shadowing or the recovery of plamasheet sources relative to the ULF wave occurrence, have a remarkable impact on the resulting structure of the belts. The overall impact of the enhanced ULF wave power is profound, but the response can be very different depending on the available source flux in the plasmasheet. We review these impacts by examining ultra-relativistic electron dynamics during seemingly different storms during the Van Allen Probe era, including during the Baker et al. third radiation belt, and show the observed behaviour can be largely explained by differences in the time sequence of events described above.

  13. Genetic diversity and structure in the Endangered Allen Cays Rock Iguana, Cyclura cychlura inornata.

    PubMed

    Aplasca, Andrea C; Iverson, John B; Welch, Mark E; Colosimo, Giuliano; Hekkala, Evon R

    2016-01-01

    The Endangered Allen Cays Rock Iguana (Cyclura cychlura inornata) is endemic to the Allen Cays, a tiny cluster of islands in the Bahamas. Naturally occurring populations exist on only two cays (<4 ha each). However, populations of unknown origin were recently discovered on four additional cays. To investigate patterns of genetic variation among these populations, we analyzed nuclear and mitochondrial markers for 268 individuals. Analysis of three mitochondrial gene regions (2,328 bp) and data for eight nuclear microsatellite loci indicated low genetic diversity overall. Estimates of effective population sizes based on multilocus genotypes were also extremely low. Despite low diversity, significant population structuring and variation in genetic diversity measures were detected among cays. Genetic data confirm the source population for an experimentally translocated population while raising concerns regarding other, unauthorized, translocations. Reduced heterozygosity is consistent with a documented historical population decline due to overharvest. This study provides the first range-wide genetic analysis of this subspecies. We suggest strategies to maximize genetic diversity during ongoing recovery including additional translocations to establish assurance populations and additional protective measures for the two remaining natural populations. PMID:26989628

  14. Marine ecological-risk assessment pilot study for Allen Harbor, Narragansett Bay, Rhode Island. Professional paper

    SciTech Connect

    Johnston, R.K.; Munns, W.R.; Mueller, C.; Nelson, W.G.; Pesch, G.G.

    1992-01-01

    An ecological risk assessment framework was applied to characterize aquatic risks associated with hazardous waste disposal at Naval Construction Battalion Center (NCBC) Davisville, Rhode Island. An initial screening phase (I) assessed exposure and related that exposure to toxicological endpoints for bivalves, amphipods, sea urchins, and biomarker assays. Results showed little evidence of major contamination in sediments or tissues except for relatively high levels of polychlorinated biphenols (PBC), butyltins compounds (TBT), and fecal coliforms observed in Allen Harbor. Effects were detected in mussel physiology, sea urchin fertilization and development, biomarker responses, and soft shell clam histology. Possible sources of contamination and toxicity from the landfill leachate, surface runoff, and recreational boating were examined using a temporaland spatial sampling scheme. Chemical and toxicological information obtained implicated all three sources as affecting Allen Harbor water quality. Laboratory bioassays of landfill exposure media, employing a variety of marine species using acute and chronic endpoints, are being used to provide data for the development of an exposure-response model for risk to the marine environment. The model will define current risk and provide an interpretive framework for long-term monitoring.

  15. From the IGY to the IHY: A Changing View of the Van Allen Radiation Belts

    NASA Astrophysics Data System (ADS)

    Hudson, M. K.

    2006-12-01

    Discovery of the Van Allen radiation belts by instrumentation flown on Explorer 1 in 1958 was the first major discovery of the Space Age. A view of the belts as static inner and outer zones of energetic particles with different sources, a double-doughnut encircling the Earth, became iconic to the point that their dynamic behavior and solar connection receded from public awareness and apparent scientific import. Then the Cycle 23 maximum in solar activity arrived in 1989-1991, the first approaching the activity level of the International Geophysical Year of 1957-58, when the Van Allen belts were first discovered. Delay in launch of the NASA-Air Force Combined Radiation Release and Effects Satellite, following the Challenger accident in 1986, led to having the right instruments in the right orbit at the right time to detect prompt injection of outer belt electrons and solar energetic protons into the `slot region' between the inner and outer belts, forming new trapped populations which lasted for years in an otherwise benign location. This event in March 1991, along with the great geomagnetic storm of March 1989, and our increased dependence on space technology since the early Explorer days, led to a resurgence of interest in the Van Allen radiation belts and understanding of their connectivity to the Sun. Additional instrumentation from NASA's International Solar Terrestrial Physics Program, the Solar Anomalous and Magnetospheric Particle Explorer (SAMPEX) and IMAGE spacecraft from the Explorer program, NOAA and DOD spacecraft, and improved worldwide linkages of groundbased measurements have contributed much since 1991 to our understanding of the dynamic characteristics of the Van Allen belts. Further, the presence of continuous solar wind measurements beginning with the launch of WIND in 1994, and SOHO images of Coronal Mass Ejections and coronal hole sources of high speed solar wind flow have filled in the connection with solar activity qualitatively anticipated

  16. Microgloma Sanders & Allen, 1973 (Nuculanidae) and Pristigloma Dall, 1900 (Pristiglomidae) (Pelecypoda) in the Campos Basin off Brazil

    PubMed Central

    Benaim, Natalia Pereira; Absalão, Ricardo Silva

    2011-01-01

    Abstract As a secondary result of oil prospecting in Brazil, samples from the Campos Basin continental slope became available. In these samples, specimens of the genera Microgloma Sanders & Allen, 1973 and Pristigloma Dall, 1900 were found. This contribution provides the southernmost record of the genus Microgloma, the first record of Microgloma mirmidina (Dautzenberg & Fischer 1897) from the western Atlantic, the descriptions of Microgloma macaron sp. n. and Microgloma nhanduti sp. n.as new species, and the shallowest record of Pristigloma alba Sanders & Allen 1973. PMID:22287903

  17. Allylic and Allenic Halide Synthesis via NbCl5- and NbBr5-Mediated Alkoxide Rearrangements

    PubMed Central

    Ravikumar, P. C.; Yao, Lihua; Fleming, Fraser F.

    2009-01-01

    Addition of NbCl5, or NbBr5, to a series of magnesium, lithium, or potassium allylic or propargylic alkoxides directly provides allylic or allenic halides. Halogenation formally occurs through a metalla-halo-[3,3] rearrangement although concerted, ionic, and direct displacement mechanisms appear to operate competitively. Transposition of the olefin is equally effective for allylic alkoxides prepared by nucleophilic addition, deprotonation, or reduction. Experimentally, the niobium pentahalide halogenations are rapid, afford essentially pure E-allylic or allenic halides after extraction, and are applicable to a range of aliphatic and aromatic alcohols, aldehydes, and ketones. PMID:19739606

  18. Allylic and allenic halide synthesis via NbCl(5)- and NbBr(5)-mediated alkoxide rearrangements.

    PubMed

    Ravikumar, P C; Yao, Lihua; Fleming, Fraser F

    2009-10-01

    Addition of NbCl(5) or NbBr(5) to a series of magnesium, lithium, or potassium allylic or propargylic alkoxides directly provides allylic or allenic halides. Halogenation formally occurs through a metalla-halo-[3,3] rearrangement, although concerted, ionic, and direct displacement mechanisms appear to operate competitively. Transposition of the olefin is equally effective for allylic alkoxides prepared by nucleophilic addition, deprotonation, or reduction. Experimentally, the niobium pentahalide halogenations are rapid, afford essentially pure (E)-allylic or -allenic halides after extraction, and are applicable to a range of aliphatic and aromatic alcohols, aldehydes, and ketones. PMID:19739606

  19. Use of a New Spirophosphine to Achieve Catalytic Enantioselective [4+1] Annulations of Amines with Allenes to Generate Dihydropyrroles

    PubMed Central

    Kramer, Søren; Fu, Gregory C.

    2015-01-01

    Due in part to the common occurrence of five-membered nitrogen heterocycles in bioactive molecules, the discovery of methods for the enantioselective synthesis of such structures is a useful endeavor. Building on a single example by Tong of a phosphine-catalyzed [4+1] annulation of an amine with an allene that furnished an achiral dihydropyrrole in 22% yield, we have developed, with the aid of a new chiral spirophosphine catalyst, a method with increased utility, specifically, improved yield, enhanced scope (the use of γ-substituted allenes), and good ee. The enantioenriched dihydropyrrole products can be transformed into other interesting families of compounds with very good stereoselectivity. PMID:25780940

  20. On the generation of large amplitude spiky solitons by ultralow frequency earthquake emission in the Van Allen radiation belt

    SciTech Connect

    Mofiz, U. A.

    2006-08-15

    The parametric coupling between earthquake emitted circularly polarized electromagnetic radiation and ponderomotively driven ion-acoustic perturbations in the Van Allen radiation belt is considered. A cubic nonlinear Schroedinger equation for the modulated radiation envelope is derived, and then solved analytically. For ultralow frequency earthquake emissions large amplitude spiky supersonic bright solitons or subsonic dark solitons are found to be generated in the Van Allen radiation belt, detection of which can be a tool for the prediction of a massive earthquake may be followed later.

  1. Atlas-based segmentation of brainstem regions in neuromelanin-sensitive magnetic resonance images

    NASA Astrophysics Data System (ADS)

    Puigvert, Marc; Castellanos, Gabriel; Uranga, Javier; Abad, Ricardo; Fernández-Seara, María. A.; Pastor, Pau; Pastor, María. A.; Muñoz-Barrutia, Arrate; Ortiz de Solórzano, Carlos

    2015-03-01

    We present a method for the automatic delineation of two neuromelanin rich brainstem structures -substantia nigra pars compacta (SN) and locus coeruleus (LC)- in neuromelanin sensitive magnetic resonance images of the brain. The segmentation method uses a dynamic multi-image reference atlas and a pre-registration atlas selection strategy. To create the atlas, a pool of 35 images of healthy subjects was pair-wise pre-registered and clustered in groups using an affinity propagation approach. Each group of the atlas is represented by a single exemplar image. Each new target image to be segmented is registered to the exemplars of each cluster. Then all the images of the highest performing clusters are enrolled into the final atlas, and the results of the registration with the target image are propagated using a majority voting approach. All registration processes used combined one two-stage affine and one elastic B-spline algorithm, to account for global positioning, region selection and local anatomic differences. In this paper, we present the algorithm, with emphasis in the atlas selection method and the registration scheme. We evaluate the performance of the atlas selection strategy using 35 healthy subjects and 5 Parkinson's disease patients. Then, we quantified the volume and contrast ratio of neuromelanin signal of these structures in 47 normal subjects and 40 Parkinson's disease patients to confirm that this method can detect neuromelanin-containing neurons loss in Parkinson's disease patients and could eventually be used for the early detection of SN and LC damage.

  2. Crystallization and Preliminary X-ray Analysis of Allene Oxide Synthase, Cytochrome P450 CYP74A2, from Parthenium argentatum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Oxylipins are oxygenated derivatives of fatty acids and pivotal signaling molecules in plants and animals. Allene oxide synthase (AOS) is a key cytochrome P450 CYP74 enzyme involved in the biosynthesis of plant oxylipin jasmonates to convert 13(S)-hydroperoxide to allene oxide. Guayule (Parthenium a...

  3. Big Sky Carbon Atlas

    DOE Data Explorer

    The Big Sky Carbon Atlas is an online geoportal designed for you to discover, interpret, and access geospatial data and maps relevant to decision support and education on carbon sequestration in the Big Sky Region. In serving as the public face of the Partnership's spatial Data Libraries, the Atlas provides a gateway to geographic information characterizing CO2 sources, potential geologic sinks, terrestrial carbon fluxes, civil and energy infrastructure, energy use, and related themes. In addition to directly serving the BSCSP and its stakeholders, the Atlas feeds regional data to the NatCarb Portal, contributing to a national perspective on carbon sequestration. Established components of the Atlas include a gallery of thematic maps and an interactive map that allows you to: • Navigate and explore regional characterization data through a user-friendly interface • Print your map views or publish them as PDFs • Identify technical references relevant to specific areas of interest • Calculate straight-line or pipeline-constrained distances from point sources of CO2 to potential geologic sink features • Download regional data layers (feature under development) (Acknowledgment to the Big Sky Carbon Sequestration Partnership (BSCSP); see home page at http://www.bigskyco2.org/)

  4. An Icelandic wind atlas

    NASA Astrophysics Data System (ADS)

    Nawri, Nikolai; Nína Petersen, Gudrun; Bjornsson, Halldór; Arason, Þórður; Jónasson, Kristján

    2013-04-01

    While Iceland has ample wind, its use for energy production has been limited. Electricity in Iceland is generated from renewable hydro- and geothermal source and adding wind energy has not be considered practical or even necessary. However, adding wind into the energy mix is becoming a more viable options as opportunities for new hydro or geothermal power installation become limited. In order to obtain an estimate of the wind energy potential of Iceland a wind atlas has been developed as a part of the Nordic project "Improved Forecast of Wind, Waves and Icing" (IceWind). The atlas is based on mesoscale model runs produced with the Weather Research and Forecasting (WRF) Model and high-resolution regional analyses obtained through the Wind Atlas Analysis and Application Program (WAsP). The wind atlas shows that the wind energy potential is considerable. The regions with the strongest average wind are nevertheless impractical for wind farms, due to distance from road infrastructure and power grid as well as harsh winter climate. However, even in easily accessible regions wind energy potential in Iceland, as measured by annual average power density, is among the highest in Western Europe. There is a strong seasonal cycle, with wintertime power densities throughout the island being at least a factor of two higher than during summer. Calculations show that a modest wind farm of ten medium size turbines would produce more energy throughout the year than a small hydro power plants making wind energy a viable additional option.

  5. Atlas of NATO.

    ERIC Educational Resources Information Center

    Young, Harry F.

    This atlas provides basic information about the North Atlantic Treaty Organization (NATO). Formed in response to growing concern for the security of Western Europe after World War II, NATO is a vehicle for Western efforts to reduce East-West tensions and the level of armaments. NATO promotes political and economic collaboration as well as military…

  6. MRIVIEW: An interactive computational tool for investigation of brain structure and function

    SciTech Connect

    Ranken, D.; George, J.

    1993-12-31

    MRIVIEW is a software system which uses image processing and visualization to provide neuroscience researchers with an integrated environment for combining functional and anatomical information. Key features of the software include semi-automated segmentation of volumetric head data and an interactive coordinate reconciliation method which utilizes surface visualization. The current system is a precursor to a computational brain atlas. We describe features this atlas will incorporate, including methods under development for visualizing brain functional data obtained from several different research modalities.

  7. Effect of data normalization on the creation of neuro-probabilistic atlases.

    PubMed

    D'Haese, Pierre-François; Pallavaram, Srivatsan; Kao, Chris; Neimat, Joseph S; Konrad, Peter E; Dawant, Benoit M

    2013-01-01

    In the past 15 years, rapid improvements in imaging technology and methodology have had a tremendous impact on how we study the human brain. During deep brain stimulation surgeries, detailed anatomical images can be combined with physiological data obtained by microelectrode recordings and microstimulations to address questions relating to the location of specific motor or sensorial functions. The main advantage of techniques such as microelectrode recordings and microstimulations over brain imaging is their ability to localize patient physiological activity with a high degree of spatial resolution. Aggregating data acquired from large populations permits to build what are commonly referred to as statistical atlases. Data points from statistical atlases can be combined to produce probabilistic maps. A crucial step in this process is the intersubject spatial normalization that is required to relate a position in one subject's brain to a position in another subject's brain. In this paper, we study the impact of spatial normalization techniques on building statistical atlases. We find that the Talairach or anterior-posterior commissure coordinate system commonly used in the medical literature produces atlases that are more dispersed than those obtained with normalization methods that rely on nonlinear volumetric image registration. We also find that the maps produced using nonlinear techniques correlate with their expected anatomic positions. PMID:23445926

  8. JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases

    PubMed Central

    Feng, Guangjie; Burton, Nick; Hill, Bill; Davidson, Duncan; Kerwin, Janet; Scott, Mark; Lindsay, Susan; Baldock, Richard

    2005-01-01

    Background Many three-dimensional (3D) images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are available for viewing this data ranging from commercial visualization packages to freely available, typically system architecture dependent, solutions. Here we discuss an atlas viewer implemented to run on any workstation using the architecture neutral Java programming language. Results We report the development of a freely available Java based viewer for 3D image data, descibe the structure and functionality of the viewer and how automated tools can be developed to manage the Java Native Interface code. The viewer allows arbitrary re-sectioning of the data and interactive browsing through the volume. With appropriately formatted data, for example as provided for the Electronic Atlas of the Developing Human Brain, a 3D surface view and anatomical browsing is available. The interface is developed in Java with Java3D providing the 3D rendering. For efficiency the image data is manipulated using the Woolz image-processing library provided as a dynamically linked module for each machine architecture. Conclusion We conclude that Java provides an appropriate environment for efficient development of these tools and techniques exist to allow computationally efficient image-processing libraries to be integrated relatively easily. PMID:15757508

  9. Brain Science, Brain Fiction.

    ERIC Educational Resources Information Center

    Bruer, John T.

    1998-01-01

    Three big ideas from brain science have arisen during the past 20 to 30 years: neural connections form rapidly early in life; critical periods occur in development; and enriched environments profoundly affect brain development during the early years. Current brain research has little to offer educational practice or policy. (10 references) (MLH)

  10. Internet-based atlas of the primate spinal cord.

    PubMed

    Tokuno, Hironobu; Tanaka, Ikuko; Senoo, Aya; Umitsu, Yoshitomo; Akazawa, Toshikazu; Nakamura, Yasuhisa; Watson, Charles

    2011-05-01

    In 2009, we reported an online brain atlas of the common marmoset (Callithrix jacchus) at http://marmoset-brain.org:2008. Here we report new digital images of the primate spinal cord sections added to the website. We prepared histological sections of every segment of the spinal cord of the common marmoset, rhesus monkey and Japanese monkey with various staining techniques. The sections were scanned with Carl Zeiss MIRAX SCAN at light microscopic resolution. Obtained digital data were processed and converted into multi-resolutionary images with Adobe Photoshop and Zoomify Design. These images of the primate spinal cords are now available on the web via the Internet. PMID:21291922

  11. MRI-based treatment planning with pseudo CT generated through atlas registration

    SciTech Connect

    Uh, Jinsoo Merchant, Thomas E.; Hua, Chiaho; Li, Yimei; Li, Xingyu

    2014-05-15

    Purpose: To evaluate the feasibility and accuracy of magnetic resonance imaging (MRI)-based treatment planning using pseudo CTs generated through atlas registration. Methods: A pseudo CT, providing electron density information for dose calculation, was generated by deforming atlas CT images previously acquired on other patients. The authors tested 4 schemes of synthesizing a pseudo CT from single or multiple deformed atlas images: use of a single arbitrarily selected atlas, arithmetic mean process using 6 atlases, and pattern recognition with Gaussian process (PRGP) using 6 or 12 atlases. The required deformation for atlas CT images was derived from a nonlinear registration of conjugated atlas MR images to that of the patient of interest. The contrasts of atlas MR images were adjusted by histogram matching to reduce the effect of different sets of acquisition parameters. For comparison, the authors also tested a simple scheme assigning the Hounsfield unit of water to the entire patient volume. All pseudo CT generating schemes were applied to 14 patients with common pediatric brain tumors. The image similarity of real patient-specific CT and pseudo CTs constructed by different schemes was compared. Differences in computation times were also calculated. The real CT in the treatment planning system was replaced with the pseudo CT, and the dose distribution was recalculated to determine the difference. Results: The atlas approach generally performed better than assigning a bulk CT number to the entire patient volume. Comparing atlas-based schemes, those using multiple atlases outperformed the single atlas scheme. For multiple atlas schemes, the pseudo CTs were similar to the real CTs (correlation coefficient, 0.787–0.819). The calculated dose distribution was in close agreement with the original dose. Nearly the entire patient volume (98.3%–98.7%) satisfied the criteria of chi-evaluation (<2% maximum dose and 2 mm range). The dose to 95% of the volume and the

  12. Acid-catalyzed isomerization of rhenium alkyne complexes to rhenium allene complexes via 1-metallacyclopropene intermediates

    SciTech Connect

    Casey, C.P.; Brady, J.T.

    1998-10-12

    The alkyne complexes C{sub 5}Me{sub 5}(CO){sub 2}Re({eta}{sup 2}-MeC{triple_bond}CMe) (1) and C{sub 5}H{sub 5}(CO){sub 2}Re({eta}{sup 2}-MeC{triple_bond}CMe) (6) underwent acid-catalyzed isomerization by way of 1-metallacyclopropene intermediates to form the allene complexes C{sub 5}Me{sub 5}(CO){sub 2}Re({eta}{sup 2}-2,3-MeHC{double_bond}C{double_bond}CH{sub 2}) (5) and C{sub 5}H{sub 5}(CO){sub 2}Re({eta}{sup 2}-2,3-MeHC{double_bond}C{double_bond}CH{sub 2}) (7). Stoichiometric reaction of 1 with CF{sub 3}CO{sub 2}H initially produced the kinetic addition product C{sub 5}Me{sub 5}(CO){sub 2}Re[{eta}{sup 2}-(Z)-MeHC{double_bond}CMeO{sub 2}CCF{sub 3}] (8-Z), which slowly isomerized to the thermodynamically more stable E isomer 8-E. The reaction of 6 with CF{sub 3}CO{sub 2}H at {minus}73 C produced only C{sub 5}H{sub 5}(CO){sub 2}Re[{eta}{sup 2}-(E)-MeHC{double_bond}CMeO{sub 2}CCF{sub 3}] (9-E), which isomerized at -60 C to a 80:20 equilibrium mixture of 9-E and 9-Z. Treatment of 9-E and 9-Z with base led to formation of allene complex 7. The rate of this elimination was independent of base concentration. Labeling studies showed that the 1-metallacyclopropene intermediate C{sub 5}H{sub 5}(CO){sub 2}({eta}{sup 2}-CMeCHMe){sup +}CF{sub 3}CO{sub 2}{sup {minus}} (12-CF{sub 3}CO{sub 2}) undergoes a number of important reactions which include, in order of decreasing relative rates: (1) addition of trifluoroacetate to give enol trifluoroacetate complexes, (2) deprotonation to give complexed allenes, (3) degenerate 1,2-hydride migrations, (4) hydride migrations to give {eta}{sup 3}-allyl complexes, and (5) deprotonation to give complexed alkynes.

  13. White matter atlas of the human spinal cord with estimation of partial volume effect.

    PubMed

    Lévy, S; Benhamou, M; Naaman, C; Rainville, P; Callot, V; Cohen-Adad, J

    2015-10-01

    Template-based analysis has proven to be an efficient, objective and reproducible way of extracting relevant information from multi-parametric MRI data. Using common atlases, it is possible to quantify MRI metrics within specific regions without the need for manual segmentation. This method is therefore free from user-bias and amenable to group studies. While template-based analysis is common procedure for the brain, there is currently no atlas of the white matter (WM) spinal pathways. The goals of this study were: (i) to create an atlas of the white matter tracts compatible with the MNI-Poly-AMU template and (ii) to propose methods to quantify metrics within the atlas that account for partial volume effect. The WM atlas was generated by: (i) digitalizing an existing WM atlas from a well-known source (Gray's Anatomy), (ii) registering this atlas to the MNI-Poly-AMU template at the corresponding slice (C4 vertebral level), (iii) propagating the atlas throughout all slices of the template (C1 to T6) using regularized diffeomorphic transformations and (iv) computing partial volume values for each voxel and each tract. Several approaches were implemented and validated to quantify metrics within the atlas, including weighted-average and Gaussian mixture models. Proof-of-concept application was done in five subjects for quantifying magnetization transfer ratio (MTR) in each tract of the atlas. The resulting WM atlas showed consistent topological organization and smooth transitions along the rostro-caudal axis. The median MTR across tracts was 26.2. Significant differences were detected across tracts, vertebral levels and subjects, but not across laterality (right-left). Among the different tested approaches to extract metrics, the maximum a posteriori showed highest performance with respect to noise, inter-tract variability, tract size and partial volume effect. This new WM atlas of the human spinal cord overcomes the biases associated with manual delineation and partial

  14. Improving atlas methodology

    USGS Publications Warehouse

    Robbins, C.S.; Dowell, B.A.; O'Brien, J.

    1987-01-01

    We are studying a sample of Maryland (2 %) and New Hampshire (4 %) Atlas blocks and a small sample in Maine. These three States used different sampling methods and block sizes. We compare sampling techniques, roadside with off-road coverage, our coverage with that of the volunteers, and different methods of quantifying Atlas results. The 7 1/2' (12-km) blocks used in the Maine Atlas are satisfactory for coarse mapping, but are too large to enable changes to be detected in the future. Most states are subdividing the standard 7 1/2' maps into six 5-km blocks. The random 1/6 sample of 5-km blocks used in New Hampshire, Vermont (published 1985), and many other states has the advantage of permitting detection of some changes in the future, but the disadvantage of leaving important habitats unsampled. The Maryland system of atlasing all 1,200 5-km blocks and covering one out of each six by quarterblocks (2 1/2-km) is far superior if enough observers can be found. A good compromise, not yet attempted, would be to Atlas a 1/6 random sample of 5-km blocks and also one other carefully selected (non-random) block on the same 7 1/2' map--the block that would include the best sample of habitats or elevations not in the random block. In our sample the second block raised the percentage of birds found from 86% of the birds recorded in the 7 1/2' quadrangle to 93%. It was helpful to list the expected species in each block and to revise this list annually. We estimate that 90-100 species could be found with intensive effort in most Maryland blocks; perhaps 95-105 in New Hampshire. It was also helpful to know which species were under-sampled so we could make a special effort to search for these. A total of 75 species per block (or 75% of the expected species in blocks with very restricted habitat diversity) is considered a practical and adequate goal in these States. When fewer than 60 species are found per block, a high proportion of the rarer species are missed, as well as some of

  15. Report on the Study of Library Use at Pitt by Professor Allen Kent, et al. (A Pittsburgh Reply).

    ERIC Educational Resources Information Center

    MacLeod, Murdo J.; Barkowski, Casimir

    This report from the Senate Library Committee at the University of Pittsburgh evaluates a widely publicized study of monograph and periodical use conducted at Pitt by Professor Allen Kent and his associates from 1975-1977. Areas of the study which are examined include structure in text and footnotes, and experimental design, execution, and…

  16. Mechanistic Aspects of the Palladium-Catalyzed Isomerization of Allenic Sulfones to 1-Arylsulfonyl 1,3-Dienes.

    PubMed

    Hampton, Carissa S; Harmata, Michael

    2016-06-01

    When an allenic sulfone is treated under palladium catalysis in the presence of a weak acid, isomerization to a 1-arylsulfonyl 1,3-diene occurs. Investigations of the mechanistic aspects of this isomerization were performed, leading to the mechanism proposed herein. Some further studies of reaction parameters are reported. PMID:27127922

  17. Van Allen Probes, NOAA, and Ground Observations of an Intense Pc 1 Wave Event Extending 12 Hours in MLT

    NASA Astrophysics Data System (ADS)

    Engebretson, M. J.; Posch, J. L.; Wygant, J. R.; Kletzing, C.; Lessard, M.; Horne, R. B.; Reeves, G. D.; Gkioulidou, M.; Fennell, J.; Oksavik, K.; Raita, T.

    2014-12-01

    On February 23, 2014 a Pc 1 wave event extending 8 hours in UT and 12 hours in MLT was observed at Halley, Antarctica and Ivalo, Finland in the dawn sector, and by both Van Allen Probes spacecraft from late morning through local noon. The wave activity was stimulated by a gradual 4-hour rise and subsequent sharp increases in solar wind pressure. Intense hydrogen band, linearly polarized Pc 1 wave activity (up to 25 nT p-p) with very similar time variations also appeared for over 4 hours at both Van Allen Probes, located ~8 and ~9 hours east of Halley. Waves appeared when these spacecraft were outside the plasmapause, with densities ~5-20 cm-3. Ten passes of NOAA-POES and METOP satellites near the northern hemisphere footpoint of the Van Allen Probes (over Siberia) show the presence of 30-80 keV subauroral proton precipitation. This is the longest-duration and most intense Pc1 event we have yet observed with the Van Allen Probes. The combination of its duration, intensity, and large local time extent (from before 02 to nearly 14 hours MLT) suggests that it might have a significant effect on the ring current, and possibly even electrons in the outer radiation belt.

  18. A Confirmatory Factor Analysis Examination of Reverse Coding Effects in Meyer and Allen's Affective and Continuance Commitment Scales.

    ERIC Educational Resources Information Center

    Magazine, Sherry L.; And Others

    1996-01-01

    Examination of the Affective and Continuance Commitment Scales of J. P. Meyer and N. J. Allen using confirmatory factor analysis for 333 subjects with the LISREL 7 computer program provided strong support across multiple diagnostics for existence of a reverse coding factor defined by the 6 negatively worded scale items. (Author/SLD)

  19. Expression of concern: A unifying mechanism for the rearrangement of vinyl allene oxide geometric isomers to cyclopentenones.

    PubMed

    Kelly, Richard

    2015-12-21

    Expression of concern for 'A unifying mechanism for the rearrangement of vinyl allene oxide geometric isomers to cyclopentenones' by Adán B. González-Pérez et al., Org. Biomol. Chem., 2014, 12, 7694-7701. PMID:26575412

  20. Remarkable new results for high-energy protons and electrons in the inner Van Allen belt regions

    NASA Astrophysics Data System (ADS)

    Baker, Daniel N.

    2016-04-01

    Early observations indicated that the Earth's Van Allen radiation belts could be separated into an inner zone dominated by high-energy protons and an outer zone dominated by high-energy electrons. Subsequent studies showed that electrons of moderate energy (less than about one megaelectronvolt) often populate both zones, with a deep 'slot' region largely devoid of particles between them. The two-belt radiation structure was explained as arising from strong electron interactions with plasmaspheric hiss just inside the plasmapause boundary with the inner edge of the outer radiation zone corresponding to the minimum plasmapause location.. Recent Van Allen Probes observations have revealed an unexpected radiation belt morphology, especially at ultrarelativistic kinetic energies (more than several megaelectronvolts). The data show an exceedingly sharp inner boundary for the ultrarelativistic electrons right at L=2.8. Additional, concurrently measured data reveal that this barrier to inward electron radial transport is likely due to scattering by powerful human electromagnetic transmitter (VLF) wave fields. We show that weak, but persistent, wave-particle pitch angle scattering deep inside the Earth's plasmasphere due to manmade signals can act to create an almost impenetrable barrier through which the most energetic Van Allen belt electrons cannot migrate. Inside of this distance, the Van Allen Probes data show that high energy (20 -100 MeV) protons have a double belt structure with a stable peak of flux at L~1.5 and a much more variable belt peaking at L~2.3.

  1. Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk from Leo Holberg and Allen Mills

    ScienceCinema

    Holberg, Leo; Mills, Allen [NIST

    2011-04-28

    Leo Holberg and Allen Mills present a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

  2. An Evaluation of the Effectiveness of the Allen Teaching Machine at the Federal Correctional Institution, Lompoc, California. Final Report.

    ERIC Educational Resources Information Center

    Ross, Harvey L.

    This study evaluated the use of the Allen group teaching machines in a basic skills program (arithmetic, language arts, General Educational Development preparation) at the Federal Correctional Institution (FCI), Lompoc, California. Out of 317 eligible inmates, 172 enrolled. The evaluator interviewed inmates, teachers, and prison administrators,…

  3. Rhodium-Catalyzed Enantioselective Intermolecular Hydroalkoxylation of Allenes and Alkynes with Alcohols: Synthesis of Branched Allylic Ethers.

    PubMed

    Liu, Zi; Breit, Bernhard

    2016-07-11

    Regio- and enantioselective additions of alcohols to either terminal allenes or internal alkynes provides access to allylic ethers by using a Rh(I) /diphenyl phosphate catalytic system. This method provides an atom-economic way to obtain chiral aliphatic and aryl allylic ethers in moderate to good yield with good to excellent enantioselectivities. PMID:27244349

  4. MARS: a mouse atlas registration system based on a planar x-ray projector and an optical camera

    NASA Astrophysics Data System (ADS)

    Wang, Hongkai; Stout, David B.; Taschereau, Richard; Gu, Zheng; Vu, Nam T.; Prout, David L.; Chatziioannou, Arion F.

    2012-10-01

    This paper introduces a mouse atlas registration system (MARS), composed of a stationary top-view x-ray projector and a side-view optical camera, coupled to a mouse atlas registration algorithm. This system uses the x-ray and optical images to guide a fully automatic co-registration of a mouse atlas with each subject, in order to provide anatomical reference for small animal molecular imaging systems such as positron emission tomography (PET). To facilitate the registration, a statistical atlas that accounts for inter-subject anatomical variations was constructed based on 83 organ-labeled mouse micro-computed tomography (CT) images. The statistical shape model and conditional Gaussian model techniques were used to register the atlas with the x-ray image and optical photo. The accuracy of the atlas registration was evaluated by comparing the registered atlas with the organ-labeled micro-CT images of the test subjects. The results showed excellent registration accuracy of the whole-body region, and good accuracy for the brain, liver, heart, lungs and kidneys. In its implementation, the MARS was integrated with a preclinical PET scanner to deliver combined PET/MARS imaging, and to facilitate atlas-assisted analysis of the preclinical PET images.

  5. Maximum-Margin Based Representation Learning from Multiple Atlases for Alzheimer’s Disease Classification

    PubMed Central

    Min, Rui; Cheng, Jian; Price, True; Wu, Guorong; Shen, Dinggang

    2015-01-01

    In order to establish the correspondences between different brains for comparison, spatial normalization based morphometric measurements have been widely used in the analysis of Alzheimer’s disease (AD). In the literature, different subjects are often compared in one atlas space, which may be insufficient in revealing complex brain changes. In this paper, instead of deploying one atlas for feature extraction and classification, we propose a maximum-margin based representation learning (MMRL) method to learn the optimal representation from multiple atlases. Unlike traditional methods that perform the representation learning separately from the classification, we propose to learn the new representation jointly with the classification model, which is more powerful in discriminating AD patients from normal controls (NC). We evaluated the proposed method on the ADNI database, and achieved 90.69% for AD/NC classification and 73.69% for p-MCI/s-MCI classification. PMID:25485381

  6. Penetration of magnetosonic waves into the plasmasphere observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Xiao, Fuliang; Zhou, Qinghua; He, Yihua; Yang, Chang; Liu, Si; Baker, D. N.; Spence, H. E.; Reeves, G. D.; Funsten, H. O.; Blake, J. B.

    2015-09-01

    During the small storm on 14-15 April 2014, Van Allen Probe A measured a continuously distinct proton ring distribution and enhanced magnetosonic (MS) waves along its orbit outside the plasmapause. Inside the plasmasphere, strong MS waves were still present but the distinct proton ring distribution was falling steeply with distance. We adopt a sum of subtracted bi-Maxwellian components to model the observed proton ring distribution and simulate the wave trajectory and growth. MS waves at first propagate toward lower L shells outside the plasmasphere, with rapidly increasing path gains related to the continuous proton ring distribution. The waves then gradually cross the plasmapause into the deep plasmasphere, with almost unchanged path gains due to the falling proton ring distribution and higher ambient density. These results present the first report on how MS waves penetrate into the plasmasphere with the aid of the continuous proton ring distributions during weak geomagnetic activities.

  7. EMIC wave spatial and coherence scales as determined from multipoint Van Allen Probe measurements

    NASA Astrophysics Data System (ADS)

    Blum, L. W.; Agapitov, O.; Bonnell, J. W.; Kletzing, C.; Wygant, J.

    2016-05-01

    Electromagnetic ion cyclotron (EMIC) waves can provide a strong source of energetic electron pitch angle scattering. These waves are often quite localized, thus their spatial extent can have a large effect on their overall scattering efficiency. Using measurements from the dual Van Allen Probes, we examine four EMIC wave events observed simultaneously on the two probes at varying spacecraft separations. Correlation of both the wave amplitude and phase observed at both spacecraft is examined to estimate the active region and coherence scales of the waves. We find well-correlated wave amplitude and amplitude modulation across distances spanning hundreds to thousands of kilometers. Phase coherence persisting 30-60 s is observable during close conjunction events but is lost as spacecraft separations exceed ~1 Earth Radii.

  8. Wave-driven butterfly distribution of Van Allen belt relativistic electrons

    SciTech Connect

    Xiao, Fuliang; Yang, Chang; Su, Zhenpeng; Zhou, Qinghua; He, Zhaoguo; He, Yihua; Baker, D. N.; Spence, H. E.; Funsten, H. O.; Blake, J. B.

    2015-10-05

    Van Allen radiation belts consist of relativistic electrons trapped by Earth's magnetic field. Trapped electrons often drift azimuthally around Earth and display a butterfly pitch angle distribution of a minimum at 90° further out than geostationary orbit. This is usually attributed to drift shell splitting resulting from day–night asymmetry in Earth’s magnetic field. However, direct observation of a butterfly distribution well inside of geostationary orbit and the origin of this phenomenon have not been provided so far. Here we report high-resolution observation that a unusual butterfly pitch angle distribution of relativistic electrons occurred within 5 Earth radii during the 28 June 2013 geomagnetic storm. In conclusion, simulation results show that combined acceleration by chorus and magnetosonic waves can successfully explain the electron flux evolution both in the energy and butterfly pitch angle distribution. Finally, the current provides a great support for the mechanism of wave-driven butterfly distribution of relativistic electrons.

  9. Convection Electric Field Observations by THEMIS and the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Califf, S.; Li, X.; Bonnell, J. W.; Wygant, J. R.; Malaspina, D.; Hartinger, M.; Thaller, S. A.

    2013-12-01

    We present direct electric field measurements made by THEMIS and the Van Allen Probes in the inner magnetosphere, focusing on the large-scale, near-DC convection electric field. The convection electric field drives plasma Earthward from the tail into the inner magnetosphere, playing a critical role in forming the ring current. Although it is normally shielded deep inside the magnetosphere, during storm times this large-scale electric field can penetrate to low L values (L < 3), eroding the plasmasphere and also providing a mechanism for ~100 keV electron injection into the slot region and inner radiation belt. The relationship of the convection electric field with the plasmasphere is also important for understanding the dynamic outer radiation belt, as the plasmapause boundary has been strongly correlated with the dynamic variation of the outer radiation belt electrons.

  10. Lobe crossing events observed by the Van Allen Probes as tests of magnetic field line mapping

    NASA Astrophysics Data System (ADS)

    Dixon, P.; MacDonald, E.; Grande, M.; Glocer, A.

    2014-04-01

    In this paper we examine a series of lobe crossing events witnessed by the twin Van Allen Probes spacecraft between 0200 and 0515 on November 14th 2012. The events occurred on the flank between 0400 and 0635 local time and at altitudes between 5.6 and 6.2 RE. During the events Dst was less than 100nT with the IMF being strongly southward (Bz = - 15nT) and eastward (By = 20 nT). Other observations at geosynchronous orbit also show lobe crossings at dawn and dusk flanks. These events provide a chance to examine the magnetic field topology in detail and compare it with models. We will show that the spacecraft were in locations with access to the open field lines by comparison to the CRCM + BATS-RUS models as well as comparing spacecraft encounters with the lobe to the predicted magnetic field topology.

  11. Long-duration exohiss waves outside the plasmasphere: observed by Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Zhu, H.; Su, Z.; Xiao, F.; Zheng, H.; Wang, Y.; He, Z.; Shen, C.; Zhang, M.; Wang, S.; Kletzing, C.; Kurth, W. S.; Hospodarsky, G. B.; Spence, H. E.; Reeves, G. D.; Funsten, H. O.; Blake, J. B.; Baker, D. N.

    2014-12-01

    We report an exohiss event in the low-density trough region observed by Van Allen Probes on 2 February 2014. These exohiss waves are discovered in the wide MLT distribution [9.1,13.4] and low magnetic latitude, with narrow-band structure and weak intensity compared with plasmaspheric hiss. Using the Continue Waveform Burst Mode data and MAG data on the EMFISIS, we analyze the normal angle, electromagnetic planarity and anti~/parallel-propagating Poynting flux of exohiss wave. The results show indicate that exohiss waves are the result of plasmaspheric hiss leakage into the trough region. The dependence of the proportion of anti~/parallel-propagating Poynting flux on MLT can be explained by Landau damping associated with suprathermal eletrons.

  12. Variability of the Inner Proton Radiation Belt Observed by Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Li, X.; Selesnick, R.; Baker, D. N.; Jaynes, A. N.; Kanekal, S. G.; Hudson, M. K.; Kress, B. T.

    2015-12-01

    Inner radiation belt protons with kinetic energy above 10 MeV are known to be highly stable, with a maximum intensity near L = 1.5 that varies little evenon solar-cycle time scales. However, for L = 2 and above, more rapid changes occur: (1) protons are trapped during solar particle events, (2) steady intensity changes near L = 2 may result from radial diffusion, (3) for L > 2 there are rapid losses during magnetic storms, and (4) the losses are replenished by albedo neutron decay. New measurements from Van Allen Probes describe each of the last three processes in detail (the first has not yet been observed). These data provide new constraints on theories of trapped proton dynamics and improved empirical estimates of transport coefficients for radiation belt modeling.

  13. "Her mouth is medicine": Beth Brant and Paula Gunn Allen's decolonizing queer erotics.

    PubMed

    Burford, Arianne

    2013-01-01

    This article asserts the need to recognize the complexity of the theoretical work of more lesbian Native American writers, focusing specifically Beth Brant (Bay of Quinte Mohawk) and Paula Gunn Allen (Laguna Pueblo). Their poetry and short stories provide a theoretically nuanced analysis of how heteronormativity is intertwined in and dependent on colonialism, and thus a methodology for Queer Theory that requires an understanding of it in relation to colonialism. They reject heteronormative Pocahontas fantasies about Native women, offering a lesbian-based tactic for decolonization through the expression of erotic desire. This article demonstrates the endless possibilities for fierce queer resistance, revolutionary change, and healing from the trauma of genocide and the accompanying colonialist heteropatriarchal disciplining of Native women's bodies. PMID:23514211

  14. Evidence for Nonlinear VLF Wave Physics from Van Allen Probe Data

    NASA Astrophysics Data System (ADS)

    Crabtree, C. E.; Tejero, E. M.; Ganguli, G.; Hospodarsky, G. B.; Kletzing, C.

    2015-12-01

    VLF waves in the whistler mode branch in the Earth's radiation belts play a critical role in both the acceleration and loss of energetic electrons. VLF waves are often observed with magnetic field amplitudes that are a significant fraction of the background magnetic field suggesting that nonlinear effects may be important. We develop new Bayesian time-series analysis tools to investigate magnetic and electric field data from the EMFISIS instrument on board the Van Allen Probes. We also validate the analysis techniques through laboratory experiments. We apply these tools to Chorus waves to show that the picture of a single coherent plane wave is insufficient to explain EMFISIS data and that nonlinear collective wave interactions play an important role in moderating Chorus wave growth. We also apply these techniques to show that nonlinear induced scattering by thermal electrons can play a significant role in controlling the propagation of large amplitude lightning generated whistlers inside the plasmasphere.

  15. The Unique Capabilities of the Allen Telescope Array for Pulsar Timing and Gravitational Wave Detection

    NASA Astrophysics Data System (ADS)

    McLaughlin, Maura

    2011-01-01

    Since their discovery in 1982, millisecond pulsars have served as exquisite probes of fundamental physics. I will discuss the most transformative current application of millisecond pulsars: the direct detection of gravitational waves. Timing an array of pulsars could result in the detection of a stochastic background of gravitational waves, most likely resulting from an ensemble of supermassive black hole binaries. The unique capabilities of the Allen Telescope Array (ATA) will make it a very important resource for this experiment. The multi-wavelength coverage will increase sensitivity and enable optimal removal of interstellar propagation affects and the flexibility of scheduling afforded by commensal observing will increase the number of sources times and the cadence at which we can observe each source. I will discuss how these properties complement existing facilities and how including the ATA will increase the sensitivity of the international pulsar timing array.

  16. Fractional Cahn-Hilliard, Allen-Cahn and porous medium equations

    NASA Astrophysics Data System (ADS)

    Akagi, Goro; Schimperna, Giulio; Segatti, Antonio

    2016-09-01

    We introduce a fractional variant of the Cahn-Hilliard equation settled in a bounded domain Ω ⊂RN and complemented with homogeneous Dirichlet boundary conditions of solid type (i.e., imposed in the whole of RN ∖ Ω). After setting a proper functional framework, we prove existence and uniqueness of weak solutions to the related initial-boundary value problem. Then, we investigate some significant singular limits obtained as the order of either of the fractional Laplacians appearing in the equation is let tend to 0. In particular, we can rigorously prove that the fractional Allen-Cahn, fractional porous medium, and fractional fast-diffusion equations can be obtained in the limit. Finally, in the last part of the paper, we discuss existence and qualitative properties of stationary solutions of our problem and of its singular limits.

  17. Wave-driven butterfly distribution of Van Allen belt relativistic electrons

    PubMed Central

    Xiao, Fuliang; Yang, Chang; Su, Zhenpeng; Zhou, Qinghua; He, Zhaoguo; He, Yihua; Baker, D. N.; Spence, H. E.; Funsten, H. O.; Blake, J. B.

    2015-01-01

    Van Allen radiation belts consist of relativistic electrons trapped by Earth's magnetic field. Trapped electrons often drift azimuthally around Earth and display a butterfly pitch angle distribution of a minimum at 90° further out than geostationary orbit. This is usually attributed to drift shell splitting resulting from day–night asymmetry in Earth's magnetic field. However, direct observation of a butterfly distribution well inside of geostationary orbit and the origin of this phenomenon have not been provided so far. Here we report high-resolution observation that a unusual butterfly pitch angle distribution of relativistic electrons occurred within 5 Earth radii during the 28 June 2013 geomagnetic storm. Simulation results show that combined acceleration by chorus and magnetosonic waves can successfully explain the electron flux evolution both in the energy and butterfly pitch angle distribution. The current provides a great support for the mechanism of wave-driven butterfly distribution of relativistic electrons. PMID:26436770

  18. Van Allen Probes Multipoint Measurements of the Spatial and Coherence Scales of EMIC Waves

    NASA Astrophysics Data System (ADS)

    Blum, L. W.; Bonnell, J. W.; Agapitov, O. V.; Bortnik, J.

    2015-12-01

    Electromagnetic ion cyclotron (EMIC) waves are able to resonate with MeV electrons and cause precipitation loss of radiation belt electrons. EMIC waves can provide a strong source of electron pitch angle diffusion, but the waves are often quite localized - thus the spatial extents of these waves can have a large effect on their overall scattering efficiency. Using measurements from the Van Allen Probes, we characterize the spatial extents of EMIC wave active regions, and how these depend on local time, radial distance, and driver. As the separation between the spacecraft along the orbital track varies in time, with one spacecraft lapping the other every ~70 days, we can determine the correlation between EMIC wave measurements at varying spacecraft separations. During individual events at close approaches (Jan 17 2013, for example - see attached figure), analysis of the detailed wave properties and coherence is performed. These studies provide important information on parameters relevant for determining resonance of EMIC waves with radiation belt electrons.

  19. George Herbert Mead and the Allen controversy at the University of Wisconsin.

    PubMed

    Cook, Gary A

    2007-01-01

    This essay uses previously unpublished correspondence of George Herbert Mead to tell the story of his involvement in the aftermath of a political dispute that took place at the University of Wisconsin during the years 1914-1915. It seeks thereby to clarify the historical significance of an article he published on this controversy in late 1915. Taken together with relevant information about the educational activities of William H. Allen of the New York Bureau of Municipal Research, Mead's correspondence and article throw helpful light upon his understanding of how an educational survey of a university should proceed; they also show how he went about the task of evaluating a failed attempt at such a survey. PMID:17205543

  20. Iridium-catalysed direct C-C coupling of methanol and allenes

    NASA Astrophysics Data System (ADS)

    Moran, Joseph; Preetz, Angelika; Mesch, Ryan A.; Krische, Michael J.

    2011-04-01

    Methanol is an abundant (35 million metric tons per year), renewable chemical feedstock, yet its use as a one-carbon building block in fine chemical synthesis is highly underdeveloped. Using a homogeneous iridium catalyst developed in our laboratory, methanol engages in a direct C-C coupling with allenes to furnish higher alcohols that incorporate all-carbon quaternary centres, free of stoichiometric by-products. A catalytic mechanism that involves turnover-limiting methanol oxidation, a consequence of the high energetic demand of methanol dehydrogenation, is corroborated through a series of competition kinetics experiments. This process represents the first catalytic C-C coupling of methanol to provide discrete products of hydrohydroxymethylation.

  1. Wave-driven butterfly distribution of Van Allen belt relativistic electrons.

    PubMed

    Xiao, Fuliang; Yang, Chang; Su, Zhenpeng; Zhou, Qinghua; He, Zhaoguo; He, Yihua; Baker, D N; Spence, H E; Funsten, H O; Blake, J B

    2015-01-01

    Van Allen radiation belts consist of relativistic electrons trapped by Earth's magnetic field. Trapped electrons often drift azimuthally around Earth and display a butterfly pitch angle distribution of a minimum at 90° further out than geostationary orbit. This is usually attributed to drift shell splitting resulting from day-night asymmetry in Earth's magnetic field. However, direct observation of a butterfly distribution well inside of geostationary orbit and the origin of this phenomenon have not been provided so far. Here we report high-resolution observation that a unusual butterfly pitch angle distribution of relativistic electrons occurred within 5 Earth radii during the 28 June 2013 geomagnetic storm. Simulation results show that combined acceleration by chorus and magnetosonic waves can successfully explain the electron flux evolution both in the energy and butterfly pitch angle distribution. The current provides a great support for the mechanism of wave-driven butterfly distribution of relativistic electrons. PMID:26436770

  2. Electron dropout echoes induced by interplanetary shock: Van Allen Probes observations

    NASA Astrophysics Data System (ADS)

    Hao, Y. X.; Zong, Q.-G.; Zhou, X.-Z.; Fu, S. Y.; Rankin, R.; Yuan, C.-J.; Lui, A. T. Y.; Spence, H. E.; Blake, J. B.; Baker, D. N.; Reeves, G. D.

    2016-06-01

    On 23 November 2012, a sudden dropout of the relativistic electron flux was observed after an interplanetary shock arrival. The dropout peaks at ˜1 MeV and more than 80% of the electrons disappeared from the drift shell. Van Allen twin Probes observed a sharp electron flux dropout with clear energy dispersion signals. The repeating flux dropout and recovery signatures, or "dropout echoes", constitute a new phenomenon referred to as a "drifting electron dropout" with a limited initial spatial range. The azimuthal range of the dropout is estimated to be on the duskside, from ˜1300 to 0100 LT. We conclude that the shock-induced electron dropout is not caused by the magnetopause shadowing. The dropout and consequent echoes suggest that the radial migration of relativistic electrons is induced by the strong dusk-dawn asymmetric interplanetary shock compression on the magnetosphere.

  3. Five Years of SETI with the Allen Telescope Array: Lessons Learned

    NASA Astrophysics Data System (ADS)

    Harp, Gerald

    2016-01-01

    We discuss recent observations at the Allen Telescope Array (ATA) supporting a wide ranging Search for Extraterrestrial Intelligence (SETI). The ATA supports observations over the frequency range 1-10 GHz with three simultaneous phased array beams used in an anticoincidence detector for false positive rejection. Here we summarize observational results over the years 2011-2015 covering multiple campaigns of exoplanet stars, the galactic plane, infrared excess targets, etc. Approximately 2 x 108 signals were identified and classified over more than 5000 hours of observation. From these results we consider various approaches to the rapid identification of human generated interference in the process of the search for a signal with origins outside the radius of the Moon's orbit. We conclude that the multi-beam technique is superb tool for answering the very difficult question of the direction of origin of signals. Data-based simulations of future instruments with more than 3 beams are compared.

  4. Real-time beamforming using high-speed FPGAs at the Allen Telescope Array

    NASA Astrophysics Data System (ADS)

    Barott, William C.; Milgrome, Oren; Wright, Melvyn; MacMahon, David; Kilsdonk, Tom; Backus, Peter; Dexter, Matt

    2011-02-01

    The Allen Telescope Array (ATA) at the Hat Creek Radio Observatory (HCRO) is a wide-field panchromatic radio telescope currently consisting of 42 offset-Gregorian antennas each with a 6 m aperture, with plans to expand the array to 350 antennas. Through unique back-end hardware, the ATA performs real-time wideband beamforming with independent subarray capabilities and customizable beam shaping. The beamformers enable science observations requiring the full gain of the array, time domain (nonintegrated) output, and interference excision or orthogonal beamsets. In this paper we report on the design of this beamformer, including architecture and experimental results. Furthermore, we address some practical considerations in large-N wideband beamformers implemented on field programmable gate array platforms, including device utilization, methods of calibration and control, and interchip synchronization.

  5. Inner zone electron radial diffusion coefficients - An update with Van Allen Probes MagEIS data

    NASA Astrophysics Data System (ADS)

    O'Brien, Paul; Fennell, Joseph; Guild, Timothy; Mazur, Joseph; Claudepierre, Seth; Clemmons, James; Turner, Drew; Blake, Bernard; Roeder, James

    2016-07-01

    Using MagEIS data from NASA's recent Van Allen Probes mission, we estimate the quiet-time radial diffusion coefficients for electrons in the inner radiation belt and slot, for energies up to ~700 keV. We provide observational evidence that energy diffusion is negligible. The main dynamic processes, then, are radial diffusion and elastic pitch angle scattering. We use a coordinate system in which these two modes of diffusion are separable. Then we integrate over pitch angle to obtain a field line content whose dynamics consist of radial diffusion and loss to the atmosphere. We estimate the loss timescale from periods of exponential decay in the time series. We then estimate the radial diffusion coefficient from the temporal and radial variation of the field line content. We show that our diffusion coefficients agree well with previously determined values. Our coefficients are consistent with diffusion by electrostatic impulses, whereas outer zone radial diffusion is thought to be dominated by electromagnetic fluctuations.

  6. Wave-driven butterfly distribution of Van Allen belt relativistic electrons

    NASA Astrophysics Data System (ADS)

    Xiao, Fuliang; Yang, Chang; Su, Zhenpeng; Zhou, Qinghua; He, Zhaoguo; He, Yihua; Baker, D. N.; Spence, H. E.; Funsten, H. O.; Blake, J. B.

    2015-10-01

    Van Allen radiation belts consist of relativistic electrons trapped by Earth's magnetic field. Trapped electrons often drift azimuthally around Earth and display a butterfly pitch angle distribution of a minimum at 90° further out than geostationary orbit. This is usually attributed to drift shell splitting resulting from day-night asymmetry in Earth's magnetic field. However, direct observation of a butterfly distribution well inside of geostationary orbit and the origin of this phenomenon have not been provided so far. Here we report high-resolution observation that a unusual butterfly pitch angle distribution of relativistic electrons occurred within 5 Earth radii during the 28 June 2013 geomagnetic storm. Simulation results show that combined acceleration by chorus and magnetosonic waves can successfully explain the electron flux evolution both in the energy and butterfly pitch angle distribution. The current provides a great support for the mechanism of wave-driven butterfly distribution of relativistic electrons.

  7. Spatial normalization of brain images and beyond.

    PubMed

    Mangin, J-F; Lebenberg, J; Lefranc, S; Labra, N; Auzias, G; Labit, M; Guevara, M; Mohlberg, H; Roca, P; Guevara, P; Dubois, J; Leroy, F; Dehaene-Lambertz, G; Cachia, A; Dickscheid, T; Coulon, O; Poupon, C; Rivière, D; Amunts, K; Sun, Z Y

    2016-10-01

    The deformable atlas paradigm has been at the core of computational anatomy during the last two decades. Spatial normalization is the variant endowing the atlas with a coordinate system used for voxel-based aggregation of images across subjects and studies. This framework has largely contributed to the success of brain mapping. Brain spatial normalization, however, is still ill-posed because of the complexity of the human brain architecture and the lack of architectural landmarks in standard morphological MRI. Multi-atlas strategies have been developed during the last decade to overcome some difficulties in the context of segmentation. A new generation of registration algorithms embedding architectural features inferred for instance from diffusion or functional MRI is on the verge to improve the architectural value of spatial normalization. A better understanding of the architectural meaning of the cortical folding pattern will lead to use some sulci as complementary constraints. Improving the architectural compliance of spatial normalization may impose to relax the diffeomorphic constraint usually underlying atlas warping. A two-level strategy could be designed: in each region, a dictionary of templates of incompatible folding patterns would be collected and matched in a way or another using rare architectural information, while individual subjects would be aligned using diffeomorphisms to the closest template. Manifold learning could help to aggregate subjects according to their morphology. Connectivity-based strategies could emerge as an alternative to deformation-based alignment leading to match the connectomes of the subjects rather than images. PMID:27344104

  8. New results from the Colorado CubeSat and comparison with Van Allen Probes data

    NASA Astrophysics Data System (ADS)

    Li, X.

    2013-05-01

    The Colorado Student Space Weather Experiment (CSSWE) is a 3-unit (10cm x 10cm x 30cm) CubeSat mission funded by the NSF, launched into a highly inclined (650) low-Earth (490km x 790km) orbit on 09/13/12 as a secondary payload under NASA's Educational Launch of Nanosatellites (ELaNa) program. CSSWE contains a single science payload, the Relativistic Electron and Proton Telescope integrated little experiment (REPTile), which is a simplified and miniaturized version of the Relativistic Electron and Proton Telescope (REPT) built at the Laboratory for Atmospheric and Space Physics (LASP) of University of Colorado for NASA/Van Allen Probes mission, which consists of two identical spacecraft, launched on 08/30/12, that traverse the heart of the radiation belts in a low inclination (100) orbit. REPTile is designed to measure the directional differential flux of protons ranging from 9 to 40 MeV and electrons from 0.5 to >3.3 MeV. Three-month science mission (full success) was completed on 1/05/13. We are now into the extended mission phase, focusing on data analysis and modeling. REPTile measures a fraction of the total population that has small enough equatorial pitch angles to reach the altitude of CSSWE, thus measuring the precipitating population as well as the trapped population. These measurements are critical for understanding the loss of outer radiation belt electrons. New results from CSSWE and comparison with Van Allen Probes data will be presented. The CSSWE is also an ideal class project, involving over 65 graduate and undergraduate students and providing training for the next generation of engineers and scientists over the full life-cycle of a satellite project.

  9. Pi2 Pulsations Observed by Van Allen Probes: A Case Study

    NASA Astrophysics Data System (ADS)

    Ghamry, E.; Kim, K. H.; Kwon, H. J.; Lee, D. H.; Kletzing, C.; Kurth, W. S.

    2014-12-01

    The plasmaspheric virtual resonance model has been proposed as one of the source mechanisms for low-latitude Pi2 pulsations. Few studies have used simultaneous multipoint observations in space to examine the spatial structure of Pi2 pulsations both inside and outside the plasmasphere. In this study we show multipoint observations for Pi2 pulsations using the Van Allen Probes (RBSP-A and RBSP-B). We focus on the two events that occurred between 1700 and 2000 UT on March 12, 2013, which were simultaneously observed by Van Allen Probes and Bohyun (BOH, L = 1.35) station in South Korea. By using plasma density measurements, we determined that during this time RBSP-A was located outside the plasmasphere and RBSP-B was located inside it. We found that the poloidal, radial (δBx) and compressional (δBz), magnetic field components, and the azimuthal (Ey) electric field component observed by both RBSP-A and RBSP-B have a high correlation with the H component at BOH for both events. The δBx and δBz oscillations at both RBSP-A and RBSP-B are nearly out of phase with ground Pi2. The Ey -H cross phases at RBSP-A outside the plasmapause and RBSP-B inside the plasmapause are nearly in quadrature for the first Pi2 event. These observations indicate that the Pi2 pulsations exist outside the plasmasphere with a radially standing signature which supports the plasmaspheric virtual resonance model.

  10. Generation and effects of EMIC waves observed by the Van Allen Probes on 18 March 2013

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Saikin, A.; Gamayunov, K. V.; Spence, H. E.; Larsen, B.; Geoffrey, R.; Smith, C. W.; Torbert, R. B.; Kurth, W. S.; Kletzing, C.

    2015-12-01

    Electromagnetic ion cyclotron (EMIC) waves play a crucial role in particle dynamics in the Earth's magnetosphere. The free energy for EMIC wave generation is usually provided by the temperature anisotropy of the energetic ring current ions. EMIC waves can in turn cause particle energization and losses through resonant wave-particle interactions. Using measurements from the Van Allen Probes, we perform a case study of EMIC waves and associated plasma conditions observed on 18 March 2013. From 0204 to 0211 UT, the Van Allen Probe-B detected He+-band EMIC wave activity in the post-midnight sector (MLT=4.6-4.9) at very low L-shells (L=2.6-2.9). The event occurred right outside the inward-pushed plasmapause in the early recovery phase of an intense geomagnetic storm - min. Dst = -132 nT at 2100 UT on 17 March 2013. During this event, the fluxes of energetic (> 1 keV), anisotropic O+ dominate both the H+ and He+ fluxes in this energy range. Meanwhile, O+ fluxes at low energies (< 0.1 keV) are low compared to H+ and He+ fluxes in the same energy range. The fluxes of <0.1 keV He+ are clearly enhanced during the wave event, indicating a signature of wave heating. To further confirm the association of the observed plasma features with the EMIC waves, we calculate the electron minimum resonant energy (Emin) and pitch angle diffusion coefficient (Dαα) of the EMIC wave packets by using nominal ion composition, derived total ion density from the frequencies of upper hybrid resonance, and measured ambient and wave magnetic field. EMIC wave growth rates are also calculated to evaluate the role of loss-cone distributed ring current ions in the EMIC wave generation.

  11. Brain herniation

    MedlinePlus

    ... herniation; Uncal herniation; Subfalcine herniation; Tonsillar herniation; Herniation - brain ... Brain herniation occurs when something inside the skull produces pressure that moves brain tissues. This is most ...

  12. ATLAS-1 Logo

    NASA Technical Reports Server (NTRS)

    1990-01-01

    The primary payload for the Space Shuttle mission STS-45, launched March 24, 1992, was the Atmospheric Laboratory for Applications and Science-1 (ATLAS-1)which was mounted on nondeployable Spacelab pallets in the orbiter cargo bay. Eight countries, th U.S., France, Germany, Belgium, United Kingdom, Switzerland, The Netherlands, and Japan, provided 12 instruments designed to perform 14 investigations in four fields. Atmospheric science instruments/investigations: Atmospheric Lyman-Alpha Emissions (ALAE); Atmospheric Trace Molecule Spectroscopy (ATMOS); Grille Spectrometer (GRILLE); Imaging Spectrometric Observatory (ISO); Millimeter-Wave Atmospheric Sounder (MAS). Solar Science: Active Cavity Radiometer Irradiance Monitor (ACRIM); Measurement of the Solar Constant (SOLCON); Solar Spectrum from 180 to 3,200 Nanometers (SOLSPEC); Solar Ultraviolet Spectral Irradiance Monitor (SUSIM). Space Plasma Physics: Atmospheric Emissions Photometric Imaging (AEPI); Space Experiments with Particle Accelerators (SEPAC). Ultraviolet astronomy: Far Ultraviolet Space Telescope (FAUST). This is the logo or emblem that was designed to represent the ATLAS-1 payload.

  13. Atlas 2 Animation

    NASA Technical Reports Server (NTRS)

    1993-01-01

    The Atmospheric Laboratory for Applications and Science-2 (ATLAS-2), was designed to collect data on the relationship between the sun's energy output and Earth's middle atmosphere and how these factors affect the ozone layer. The ATLAS-2 flew on the Space Shuttle Discovery's mission SST-56, launched on April 8, 1993. The videotape consists of an animated tour of the instruments that were included as part of the mission. The first half of the tape shows the various instruments, pointing to each in turn and identifying each by the associated initialisms. The instruments identified were: the Atmospheric Trace Molecule Spectroscopy (ATMOS), Millimeter Wave Atmospheric Sounder (MAS), Shuttle Solar Backscatter Ultraviolet/A (SSBUV/A) spectrometer, Solar Spectrum Measurement (SOLSPEC) instrument, Solar Ultraviolet Irradiance Monitor (SUSIM), Active Cavity Radiometer (ACR) and Solar Constant (SOLCON).) The second half of the animation shows the same tour without the pointing or the identification of the instruments.

  14. The ATLAS Forward Calorimeter

    NASA Astrophysics Data System (ADS)

    Artamonov, A.; Bailey, D.; Belanger, G.; Cadabeschi, M.; Chen, T.-Y.; Epshteyn, V.; Gorbounov, P.; Joo, K. K.; Khakzad, M.; Khovanskiy, V.; Krieger, P.; Loch, P.; Mayer, J.; Neuheimer, E.; Oakham, F. G.; O'Neill, M.; Orr, R. S.; Qi, M.; Rutherfoord, J.; Savine, A.; Schram, M.; Shatalov, P.; Shaver, L.; Shupe, M.; Stairs, G.; Strickland, V.; Tompkins, D.; Tsukerman, I.; Vincent, K.

    2008-02-01

    Forward calorimeters, located near the incident beams, complete the nearly 4π coverage for high pT particles resulting from proton-proton collisions in the ATLAS detector at the Large Hadron Collider at CERN. Both the technology and the deployment of the forward calorimeters in ATLAS are novel. The liquid argon rod/tube electrode structure for the forward calorimeters was invented specifically for applications in high rate environments. The placement of the forward calorimeters adjacent to the other calorimeters relatively close to the interaction point provides several advantages including nearly seamless calorimetry and natural shielding for the muon system. The forward calorimeter performance requirements are driven by events with missing ET and tagging jets.

  15. Mercury-Atlas Test Launch

    NASA Technical Reports Server (NTRS)

    1961-01-01

    A NASA Project Mercury spacecraft was test launched at 11:15 AM EST on April 25, 1961 from Cape Canaveral, Florida, in a test designed to qualify the Mercury Spacecraft and all systems, which must function during orbit and reentry from orbit. The Mercury-Atlas vehicle was destroyed by Range Safety Officer about 40 seconds after liftoff. The spacecraft was recovered and appeared to be in good condition. Atlas was designed to launch payloads into low Earth orbit, geosynchronous transfer orbit or geosynchronous orbit. NASA first launched Atlas as a space launch vehicle in 1958. Project SCORE, the first communications satellite that transmitted President Eisenhower's pre-recorded Christmas speech around the world, was launched on an Atlas. For all three robotic lunar exploration programs, Atlas was used. Atlas/ Centaur vehicles launched both Mariner and Pioneer planetary probes. The current operational Atlas II family has a 100% mission success rating. For more information about Atlas, please see Chapter 2 in Roger Launius and Dennis Jenkins' book To Reach the High Frontier published by The University Press of Kentucky in 2002.

  16. Assessment Atlas, 1982-83.

    ERIC Educational Resources Information Center

    Yosemite Community Coll. District, Modesto, CA.

    Designed to provide information of value in establishing a base for decisionmaking in the Yosemite Community College District (YCCD), this assessment atlas graphically presents statistical data on the District as a whole, its two campuses, and YCCD Central Services for 1982-83. After an introduction to the use of the assessment atlas and…

  17. Assessment Atlas, 1983-84.

    ERIC Educational Resources Information Center

    Yosemite Community Coll. District, Modesto, CA.

    Designed to provide information of value in establishing a base for decision making in the Yosemite Community College District (YCCD), this assessment atlas graphically presents statistical data for the District as a whole, its two campuses, and YCCD Central Services for 1983-84. After an introduction to the use of the assessment atlas and…

  18. ATLAS discoveries of optical transients

    NASA Astrophysics Data System (ADS)

    Tonry, J.; Denneau, L.; Stalder, B.; Heinze, A.; Sherstyuk, A.; Rest, A.; Smith, K. W.; Smartt, S. J.

    2016-03-01

    We report the following transients found by the ATLAS survey (Tonry et al. ATel #8680). ATLAS is a twin 0.5m telescope system on Haleakala and Mauna Loa. The first unit is robotically operational on Haleakala (see http://www.fallingstar.com).

  19. WESTCARB Carbon Atlas

    DOE Data Explorer

    The West Coast Regional Carbon Sequestration Partnership (known as WESTCARB) was established in Fall 2003. It is one of seven research partnerships co-funded by DOE to characterize regional carbon sequestration opportunities and conduct pilot-scale validation tests. The California Energy Commission manages WESTCARB and is a major co-funder. WESTCARB is characterizing the extent and capacity of geologic formations capable of storing CO2, known as sinks. Results are entered into a geographic information system (GIS) database, along with the location of major CO2-emitting point sources in each of the six WESTCARB states, enabling researchers and the public to gauge the proximity of candidate CO2 storage sites to emission sources and the feasibility of linking them via pipelines. Specifically, the WESTCARB GIS database (also known as the carbon atlas) stores layers of geologic information about potential underground storage sites, such as porosity and nearby fault-lines and aquifers. Researchers use these data, along with interpreted geophysical data and available oil and gas well logs to estimate the region's potential geologic storage capacity. The database also depicts existing pipeline routes and rights-of-way and lands that could be off-limits, which can aid the development of a regional carbon management strategy. The WESTCARB Carbon Atlas, which is accessible to the public, provides a resource for public discourse on practical solutions for regional CO2 management. A key WESTCARB partner, the Utah Automated Geographic Reference Center, has developed data serving procedures to enable the WESTCARB Carbon Atlas to be integrated with those from other regional partnerships, thereby supporting the U.S. Department of Energy's national carbon atlas, NATCARB

  20. Chandra Galaxy Atlas

    NASA Astrophysics Data System (ADS)

    Kim, Dong-Woo; Anderson, Craig; Burke, Doug; Fabbiano, Giuseppina; Fruscione, Antonella; Lauer, Jennifer L.; McCollough, Michael L.; Morgan, Doug; Mossman, Amy; O'Sullivan, Ewan; Paggi, Alessandro; Trinchieri, Ginevra

    2016-01-01

    We present the new results from the Chandra Galaxy Atlas prpject. We have systematically analyzed the archival Chandra data of 50 early type galaxies to study their hot ISM. Taking full advantage of the Chandra capabilities, we produced spatially resolved data products with additional spectral information. We will make these products publicly available and use them for our focused science goals, e.g., gas morphology, scaling relation, X-ray based mass profile, circum-nuclear gas.

  1. Topographical atlas sheets

    USGS Publications Warehouse

    Wheeler, George Montague

    1877-01-01

    The following topographical atlas maps, published during the year, accompany the copies of Appendix N.N. of the Annual Report of the Chief of Engineers for 1877, beinig Annual Report of Lieut. Geo. M. Wheeler, Corps of Engineers, in charge of U. S. Geographical Surveys, are in continuation of the series ninety-five in number, on a scale of 1 inch to 8 miles, embracing the territory of the United States lying west of the 100th meridian.

  2. Topographical atlas sheets

    USGS Publications Warehouse

    Wheeler, George Montague

    1876-01-01

    The following topographical atlas sheets, accompanying Appendix J.J. of the Annual Report of the Chief of Engineers, U.S. Army-being Annual Report upon U. S. Geographical Surveys-have been published during the fiscal year ending June 30, 1876, and are a portion of the series projected to embrace the territory of the United States lying west of the 100th meridian.

  3. Software-based Diffusion MR Human Brain Phantom for Evaluating Fiber-tracking Algorithms.

    PubMed

    Shi, Yundi; Roger, Gwendoline; Vachet, Clement; Budin, Francois; Maltbie, Eric; Verde, Audrey; Hoogstoel, Marion; Berger, Jean-Baptiste; Styner, Martin

    2013-03-13

    Fiber tracking provides insights into the brain white matter network and has become more and more popular in diffusion MR imaging. Hardware or software phantom provides an essential platform to investigate, validate and compare various tractography algorithms towards a "gold standard". Software phantoms excel due to their flexibility in varying imaging parameters, such as tissue composition, SNR, as well as potential to model various anatomies and pathologies. This paper describes a novel method in generating diffusion MR images with various imaging parameters from realistically appearing, individually varying brain anatomy based on predefined fiber tracts within a high-resolution human brain atlas. Specifically, joint, high resolution DWI and structural MRI brain atlases were constructed with images acquired from 6 healthy subjects (age 22-26) for the DWI data and 56 healthy subject (age 18-59) for the structural MRI data. Full brain fiber tracking was performed with filtered, two-tensor tractography in atlas space. A deformation field based principal component model from the structural MRI as well as unbiased atlas building was then employed to generate synthetic structural brain MR images that are individually varying. Atlas fiber tracts were accordingly warped into each synthetic brain anatomy. Diffusion MR images were finally computed from these warped tracts via a composite hindered and restricted model of diffusion with various imaging parameters for gradient directions, image resolution and SNR. Furthermore, an open-source program was developed to evaluate the fiber tracking results both qualitatively and quantitatively based on various similarity measures. PMID:24357914

  4. A probabilistic atlas of the basal ganglia using 7 T MRI

    PubMed Central

    Keuken, Max C.; Forstmann, Birte U.

    2015-01-01

    A common localization procedure in functional imaging studies includes the overlay of statistical parametric functional magnetic resonance imaging (fMRI) maps or coordinates with neuroanatomical atlases in standard space, e.g., MNI-space. This procedure allows the identification of specific brain regions. Most standard MRI software packages include a wide range of atlases but have a poor coverage of the subcortex. We estimated that approximately 7% of the known subcortical structures are mapped in standard MRI-compatible atlases [1]. Here we provide a data description of a subcortical probabilistic atlas based on ultra-high resolution in-vivo anatomical imaging using 7 T (T) MRI. The atlas includes six subcortical nuclei: the striatum (STR), the globus pallidus internal and external segment (GPi/e), the subthalamic nucleus (STN), the substantia nigra (SN), and the red nucleus (RN). These probabilistic atlases are shared on freely available platforms such as NITRC and NeuroVault and are published in NeuroImage “Quantifying inter-individual anatomical variability in the subcortex using 7 T structural MRI” [2]. PMID:26322322

  5. Anatomical guidance for functional near-infrared spectroscopy: AtlasViewer tutorial

    PubMed Central

    Aasted, Christopher M.; Yücel, Meryem A.; Cooper, Robert J.; Dubb, Jay; Tsuzuki, Daisuke; Becerra, Lino; Petkov, Mike P.; Borsook, David; Dan, Ippeita; Boas, David A.

    2015-01-01

    Abstract. Functional near-infrared spectroscopy (fNIRS) is an optical imaging method that is used to noninvasively measure cerebral hemoglobin concentration changes induced by brain activation. Using structural guidance in fNIRS research enhances interpretation of results and facilitates making comparisons between studies. AtlasViewer is an open-source software package we have developed that incorporates multiple spatial registration tools to enable structural guidance in the interpretation of fNIRS studies. We introduce the reader to the layout of the AtlasViewer graphical user interface, the folder structure, and user files required in the creation of fNIRS probes containing sources and detectors registered to desired locations on the head, evaluating probe fabrication error and intersubject probe placement variability, and different procedures for estimating measurement sensitivity to different brain regions as well as image reconstruction performance. Further, we detail how AtlasViewer provides a generic head atlas for guiding interpretation of fNIRS results, but also permits users to provide subject-specific head anatomies to interpret their results. We anticipate that AtlasViewer will be a valuable tool in improving the anatomical interpretation of fNIRS studies. PMID:26157991

  6. volBrain: An Online MRI Brain Volumetry System

    PubMed Central

    Manjón, José V.; Coupé, Pierrick

    2016-01-01

    The amount of medical image data produced in clinical and research settings is rapidly growing resulting in vast amount of data to analyze. Automatic and reliable quantitative analysis tools, including segmentation, allow to analyze brain development and to understand specific patterns of many neurological diseases. This field has recently experienced many advances with successful techniques based on non-linear warping and label fusion. In this work we present a novel and fully automatic pipeline for volumetric brain analysis based on multi-atlas label fusion technology that is able to provide accurate volumetric information at different levels of detail in a short time. This method is available through the volBrain online web interface (http://volbrain.upv.es), which is publically and freely accessible to the scientific community. Our new framework has been compared with current state-of-the-art methods showing very competitive results. PMID:27512372

  7. volBrain: An Online MRI Brain Volumetry System.

    PubMed

    Manjón, José V; Coupé, Pierrick

    2016-01-01

    The amount of medical image data produced in clinical and research settings is rapidly growing resulting in vast amount of data to analyze. Automatic and reliable quantitative analysis tools, including segmentation, allow to analyze brain development and to understand specific patterns of many neurological diseases. This field has recently experienced many advances with successful techniques based on non-linear warping and label fusion. In this work we present a novel and fully automatic pipeline for volumetric brain analysis based on multi-atlas label fusion technology that is able to provide accurate volumetric information at different levels of detail in a short time. This method is available through the volBrain online web interface (http://volbrain.upv.es), which is publically and freely accessible to the scientific community. Our new framework has been compared with current state-of-the-art methods showing very competitive results. PMID:27512372

  8. Van Allen Probes Mission Space Academy: Educating middle school students about Earth's mysterious radiation belts

    NASA Astrophysics Data System (ADS)

    Butler, L.; Turney, D.; Matiella Novak, A.; Smith, D.; Simon, M.

    2013-12-01

    How's the weather in space? Why on Earth did NASA send two satellites above Earth to study radiation belts and space weather? To learn the answer to questions about NASA's Van Allen Probes mission, 450 students and their teachers from Maryland middle schools attended Space Academy events highlighting the Van Allen Probes mission. Sponsored by the Applied Physics Laboratory (APL) and Discovery Education, the events are held at the APL campus in Laurel, MD. Space Academies take students and teachers on behind-the-scenes exploration of how spacecraft are built, what they are designed to study, and introduces them to the many professionals that work together to create some of NASA's most exciting projects. Moderated by a public relations representative in the format of an official NASA press conference, the daylong event includes a student press conference with students as reporters and mission experts as panelists. Lunch with mission team members gives students a chance to ask more questions. After lunch, students don souvenir clean room suits, enjoy interactive science demonstrations, and tour APL facilities where the Van Allen Probes were built and tested before launch. Students may even have an opportunity to peek inside a clean room to view spacecraft being assembled. Prior to the event, teachers are provided with classroom activities, lesson plans, and videos developed by APL and Discovery Education to help prepare students for the featured mission. The activities are aligned to National Science Education Standards and appropriate for use in the classroom. Following their visit, student journalists are encouraged to write a short article about their field trip; selections are posted on the Space Academy web site. Designed to engage, inspire, and influence attitudes about space science and STEM careers, Space Academies provide an opportunity to attract underserved populations and emphasize that space science is for everyone. Exposing students to a diverse group of

  9. Atlas-guided cluster analysis of large tractography datasets.

    PubMed

    Ros, Christian; Güllmar, Daniel; Stenzel, Martin; Mentzel, Hans-Joachim; Reichenbach, Jürgen Rainer

    2013-01-01

    Diffusion Tensor Imaging (DTI) and fiber tractography are important tools to map the cerebral white matter microstructure in vivo and to model the underlying axonal pathways in the brain with three-dimensional fiber tracts. As the fast and consistent extraction of anatomically correct fiber bundles for multiple datasets is still challenging, we present a novel atlas-guided clustering framework for exploratory data analysis of large tractography datasets. The framework uses an hierarchical cluster analysis approach that exploits the inherent redundancy in large datasets to time-efficiently group fiber tracts. Structural information of a white matter atlas can be incorporated into the clustering to achieve an anatomically correct and reproducible grouping of fiber tracts. This approach facilitates not only the identification of the bundles corresponding to the classes of the atlas; it also enables the extraction of bundles that are not present in the atlas. The new technique was applied to cluster datasets of 46 healthy subjects. Prospects of automatic and anatomically correct as well as reproducible clustering are explored. Reconstructed clusters were well separated and showed good correspondence to anatomical bundles. Using the atlas-guided cluster approach, we observed consistent results across subjects with high reproducibility. In order to investigate the outlier elimination performance of the clustering algorithm, scenarios with varying amounts of noise were simulated and clustered with three different outlier elimination strategies. By exploiting the multithreading capabilities of modern multiprocessor systems in combination with novel algorithms, our toolkit clusters large datasets in a couple of minutes. Experiments were conducted to investigate the achievable speedup and to demonstrate the high performance of the clustering framework in a multiprocessing environment. PMID:24386292

  10. Atlas-Guided Cluster Analysis of Large Tractography Datasets

    PubMed Central

    Ros, Christian; Güllmar, Daniel; Stenzel, Martin; Mentzel, Hans-Joachim; Reichenbach, Jürgen Rainer

    2013-01-01

    Diffusion Tensor Imaging (DTI) and fiber tractography are important tools to map the cerebral white matter microstructure in vivo and to model the underlying axonal pathways in the brain with three-dimensional fiber tracts. As the fast and consistent extraction of anatomically correct fiber bundles for multiple datasets is still challenging, we present a novel atlas-guided clustering framework for exploratory data analysis of large tractography datasets. The framework uses an hierarchical cluster analysis approach that exploits the inherent redundancy in large datasets to time-efficiently group fiber tracts. Structural information of a white matter atlas can be incorporated into the clustering to achieve an anatomically correct and reproducible grouping of fiber tracts. This approach facilitates not only the identification of the bundles corresponding to the classes of the atlas; it also enables the extraction of bundles that are not present in the atlas. The new technique was applied to cluster datasets of 46 healthy subjects. Prospects of automatic and anatomically correct as well as reproducible clustering are explored. Reconstructed clusters were well separated and showed good correspondence to anatomical bundles. Using the atlas-guided cluster approach, we observed consistent results across subjects with high reproducibility. In order to investigate the outlier elimination performance of the clustering algorithm, scenarios with varying amounts of noise were simulated and clustered with three different outlier elimination strategies. By exploiting the multithreading capabilities of modern multiprocessor systems in combination with novel algorithms, our toolkit clusters large datasets in a couple of minutes. Experiments were conducted to investigate the achievable speedup and to demonstrate the high performance of the clustering framework in a multiprocessing environment. PMID:24386292

  11. Atlas-based functional radiosurgery: Early results

    SciTech Connect

    Stancanello, J.; Romanelli, P.; Pantelis, E.; Sebastiano, F.; Modugno, N.

    2009-02-15

    Functional disorders of the brain, such as dystonia and neuropathic pain, may respond poorly to medical therapy. Deep brain stimulation (DBS) of the globus pallidus pars interna (GPi) and the centromedian nucleus of the thalamus (CMN) may alleviate dystonia and neuropathic pain, respectively. A noninvasive alternative to DBS is radiosurgical ablation [internal pallidotomy (IP) and medial thalamotomy (MT)]. The main technical limitation of radiosurgery is that targets are selected only on the basis of MRI anatomy, without electrophysiological confirmation. This means that, to be feasible, image-based targeting must be highly accurate and reproducible. Here, we report on the feasibility of an atlas-based approach to targeting for functional radiosurgery. In this method, masks of the GPi, CMN, and medio-dorsal nucleus were nonrigidly registered to patients' T1-weighted MRI (T1w-MRI) and superimposed on patients' T2-weighted MRI (T2w-MRI). Radiosurgical targets were identified on the T2w-MRI registered to the planning CT by an expert functional neurosurgeon. To assess its feasibility, two patients were treated with the CyberKnife using this method of targeting; a patient with dystonia received an IP (120 Gy prescribed to the 65% isodose) and a patient with neuropathic pain received a MT (120 Gy to the 77% isodose). Six months after treatment, T2w-MRIs and contrast-enhanced T1w-MRIs showed edematous regions around the lesions; target placements were reevaluated by DW-MRIs. At 12 months post-treatment steroids for radiation-induced edema and medications for dystonia and neuropathic pain were suppressed. Both patients experienced significant relief from pain and dystonia-related problems. Fifteen months after treatment edema had disappeared. Thus, this work shows promising feasibility of atlas-based functional radiosurgery to improve patient condition. Further investigations are indicated for optimizing treatment dose.

  12. Predicting aphasia type from brain damage measured with structural MRI.

    PubMed

    Yourganov, Grigori; Smith, Kimberly G; Fridriksson, Julius; Rorden, Chris

    2015-12-01

    Chronic aphasia is a common consequence of a left-hemisphere stroke. Since the early insights by Broca and Wernicke, studying the relationship between the loci of cortical damage and patterns of language impairment has been one of the concerns of aphasiology. We utilized multivariate classification in a cross-validation framework to predict the type of chronic aphasia from the spatial pattern of brain damage. Our sample consisted of 98 patients with five types of aphasia (Broca's, Wernicke's, global, conduction, and anomic), classified based on scores on the Western Aphasia Battery (WAB). Binary lesion maps were obtained from structural MRI scans (obtained at least 6 months poststroke, and within 2 days of behavioural assessment); after spatial normalization, the lesions were parcellated into a disjoint set of brain areas. The proportion of damage to the brain areas was used to classify patients' aphasia type. To create this parcellation, we relied on five brain atlases; our classifier (support vector machine - SVM) could differentiate between different kinds of aphasia using any of the five parcellations. In our sample, the best classification accuracy was obtained when using a novel parcellation that combined two previously published brain atlases, with the first atlas providing the segmentation of grey matter, and the second atlas used to segment the white matter. For each aphasia type, we computed the relative importance of different brain areas for distinguishing it from other aphasia types; our findings were consistent with previously published reports of lesion locations implicated in different types of aphasia. Overall, our results revealed that automated multivariate classification could distinguish between aphasia types based on damage to atlas-defined brain areas. PMID:26465238

  13. Simultaneous Pi2 observations by the Van Allen Probes inside and outside the plasmasphere

    NASA Astrophysics Data System (ADS)

    Ghamry, E.; Kim, K.-H.; Kwon, H.-J.; Lee, D.-H.; Park, J.-S.; Choi, J.; Hyun, K.; Kurth, W. S.; Kletzing, C.; Wygant, J. R.; Huang, J.

    2015-06-01

    Plasmaspheric virtual resonance (PVR) model has been proposed as one of source mechanisms for low-latitude Pi2 pulsations. Since PVR-associated Pi2 pulsations are not localized inside the plasmasphere, simultaneous multipoint observations inside and outside the plasmasphere require to test the PVR model. Until now, however, there are few studies using simultaneous multisatellite observations inside and outside the plasmasphere for understanding the radial structure of Pi2 pulsation. In this study, we focus on the Pi2 event observed at low-latitude Bohyun (BOH, L = 1.35) ground station in South Korea in the postmidnight sector (magnetic local time (MLT) = 3.0) for the interval from 1730 to 1900 UT on 12 March 2013. By using electron density derived from the frequency of the upper hybrid waves detected at Van Allen Probe-A (VAP-A) and Van Allen Probe-B (VAP-B), the plasmapause is identified. At the time of the Pi2 event, VAP-A was outside the plasmasphere near midnight (00:55 MLT and L =˜ 6), while VAP-B was inside the plasmasphere in the postmidnight sector (02:15 MLT and L =˜ 5). VAP-B observed oscillations in the compressional magnetic field component (Bz) and the dawn-to-dusk electric field component (Ey), having high coherence with the BOH Pi2 pulsation in the H component. The H-Bz and H-Ey cross phases at VAP-B inside the plasmasphere were near -180° and -90°, respectively. These phase relationships among Bz, Ey, and H are consistent with a radially standing oscillation of the fundamental mode reported in previous studies. At VAP-A outside the plasmasphere, Bz oscillations were highly correlated with BOH Pi2 pulsations with ˜-180° phase delay, and the H-Ey cross phase is near -90°. From these two-satellite observations, we suggest that the fundamental PVR mode is directly detected by VAP-A and VAP-B.

  14. Multi-atlas segmentation with joint label fusion and corrective learning—an open source implementation

    PubMed Central

    Wang, Hongzhi; Yushkevich, Paul A.

    2013-01-01

    Label fusion based multi-atlas segmentation has proven to be one of the most competitive techniques for medical image segmentation. This technique transfers segmentations from expert-labeled images, called atlases, to a novel image using deformable image registration. Errors produced by label transfer are further reduced by label fusion that combines the results produced by all atlases into a consensus solution. Among the proposed label fusion strategies, weighted voting with spatially varying weight distributions derived from atlas-target intensity similarity is a simple and highly effective label fusion technique. However, one limitation of most weighted voting methods is that the weights are computed independently for each atlas, without taking into account the fact that different atlases may produce similar label errors. To address this problem, we recently developed the joint label fusion technique and the corrective learning technique, which won the first place of the 2012 MICCAI Multi-Atlas Labeling Challenge and was one of the top performers in 2013 MICCAI Segmentation: Algorithms, Theory and Applications (SATA) challenge. To make our techniques more accessible to the scientific research community, we describe an Insight-Toolkit based open source implementation of our label fusion methods. Our implementation extends our methods to work with multi-modality imaging data and is more suitable for segmentation problems with multiple labels. We demonstrate the usage of our tools through applying them to the 2012 MICCAI Multi-Atlas Labeling Challenge brain image dataset and the 2013 SATA challenge canine leg image dataset. We report the best results on these two datasets so far. PMID:24319427

  15. Multi-atlas segmentation with joint label fusion and corrective learning-an open source implementation.

    PubMed

    Wang, Hongzhi; Yushkevich, Paul A

    2013-01-01

    Label fusion based multi-atlas segmentation has proven to be one of the most competitive techniques for medical image segmentation. This technique transfers segmentations from expert-labeled images, called atlases, to a novel image using deformable image registration. Errors produced by label transfer are further reduced by label fusion that combines the results produced by all atlases into a consensus solution. Among the proposed label fusion strategies, weighted voting with spatially varying weight distributions derived from atlas-target intensity similarity is a simple and highly effective label fusion technique. However, one limitation of most weighted voting methods is that the weights are computed independently for each atlas, without taking into account the fact that different atlases may produce similar label errors. To address this problem, we recently developed the joint label fusion technique and the corrective learning technique, which won the first place of the 2012 MICCAI Multi-Atlas Labeling Challenge and was one of the top performers in 2013 MICCAI Segmentation: Algorithms, Theory and Applications (SATA) challenge. To make our techniques more accessible to the scientific research community, we describe an Insight-Toolkit based open source implementation of our label fusion methods. Our implementation extends our methods to work with multi-modality imaging data and is more suitable for segmentation problems with multiple labels. We demonstrate the usage of our tools through applying them to the 2012 MICCAI Multi-Atlas Labeling Challenge brain image dataset and the 2013 SATA challenge canine leg image dataset. We report the best results on these two datasets so far. PMID:24319427

  16. ATLAS 1: Encountering Planet Earth

    NASA Technical Reports Server (NTRS)

    Shea, Charlotte; Mcmahan, Tracy; Accardi, Denise; Tygielski, Michele; Mikatarian, Jeff; Wiginton, Margaret (Editor)

    1984-01-01

    Several NASA science programs examine the dynamic balance of sunlight, atmosphere, water, land, and life that governs Earth's environment. Among these is a series of Space Shuttle-Spacelab missions, named the Atmospheric Laboratory for Applications and Science (ATLAS). During the ATLAS missions, international teams of scientists representing many disciplines combine their expertise to seek answers to complex questions about the atmospheric and solar conditions that sustain life on Earth. The ATLAS program specifically investigates how Earth's middle atmosphere and upper atmospheres and climate are affected by both the Sun and by products of industrial and agricultural activities on Earth.

  17. Automated Loads Analysis System (ATLAS)

    NASA Technical Reports Server (NTRS)

    Gardner, Stephen; Frere, Scot; O’Reilly, Patrick

    2013-01-01

    ATLAS is a generalized solution that can be used for launch vehicles. ATLAS is used to produce modal transient analysis and quasi-static analysis results (i.e., accelerations, displacements, and forces) for the payload math models on a specific Shuttle Transport System (STS) flight using the shuttle math model and associated forcing functions. This innovation solves the problem of coupling of payload math models into a shuttle math model. It performs a transient loads analysis simulating liftoff, landing, and all flight events between liftoff and landing. ATLAS utilizes efficient and numerically stable algorithms available in MSC/NASTRAN.

  18. Synthesis of 1,3-Dienes via a Sequential Suzuki-Miyaura Coupling/Palladium-Mediated Allene Isomerization Sequence.

    PubMed

    Al-Jawaheri, Yassir; Kimber, Marc C

    2016-07-15

    We report a facile method for the synthesis of 1,3-dienes by a sequential process consisting of a palladium-catalyzed, base-free, Suzuki-Miyaura coupling/isomerization sequence. This sequence couples boronic acids with propargyl alcohols, generating the requisite allene in situ, followed by conversion of the unactivated allene to its 1,3-diene via a hydro-palladation/dehydro-palladation process. This process is general for a range of boronic acids, including boronic acids with electron-donating and -withdrawing groups, as well as heteroarylboronic acids. Key to this process is the boric acid byproduct of the base-free Suzuki-Miyauru coupling, which generates the required palladium-hydrido complex [H-Pd(II)-OB(OH)2] required for the isomerization. PMID:27355240

  19. Generalized Debye-Peierls/Allen-Feldman model for the lattice thermal conductivity of low-dimensional and disordered materials

    NASA Astrophysics Data System (ADS)

    Zhu, Taishan; Ertekin, Elif

    2016-04-01

    We present a generalized model to describe the lattice thermal conductivity of low-dimensional (low-D) and disordered systems. The model is a straightforward generalization of the Debye-Peierls and Allen-Feldman schemes to arbitrary dimensions, accounting for low-D effects such as differences in dispersion, density of states, and scattering. Similar in spirit to the Allen-Feldman approach, heat carriers are categorized according to their transporting capacity as propagons, diffusons, and locons. The results of the generalized model are compared to experimental results when available, and equilibrium molecular dynamics simulations otherwise. The results are in very good agreement with our analysis of phonon localization in disordered low-D systems, such as amorphous graphene and glassy diamond nanothreads. Several unique aspects of thermal transport in low-D and disordered systems, such as milder suppression of thermal conductivity and negligible diffuson contributions, are captured by the approach.

  20. The role of ring current particle injections: Global simulations and Van Allen Probes observations during 17 March 2013 storm

    NASA Astrophysics Data System (ADS)

    Yu, Yiqun; Jordanova, Vania; Welling, Dan; Larsen, Brian; Claudepierre, Seth G.; Kletzing, Craig

    2014-02-01

    We simulate substorm injections observed by the Van Allen Probes during the 17 March 2013 storm using a self-consistent coupling between the ring current model RAM-SCB and the global MHD model BATS-R-US. This is a significant advancement compared to previous studies that used artificially imposed electromagnetic field pulses to mimic substorm dipolarization and associated inductive electric field. Several substorm dipolarizations and injections are reproduced in the MHD model, in agreement with the timing of shape changes in the AE/AL index. The associated inductive electric field transports plasma sheet plasma to geostationary altitudes, providing the boundary plasma source to the ring current model. It is found that impulsive plasma sheet injections, together with a large-scale convection electric field, are necessary to develop a strong ring current. Comparisons with Van Allen Probes observations show that our model reasonably well captures dispersed electron injections and the global Dst index.